diff --git a/client/src/pages/settings.tsx b/client/src/pages/settings.tsx
index df7cf7d..890b767 100644
--- a/client/src/pages/settings.tsx
+++ b/client/src/pages/settings.tsx
@@ -1118,6 +1118,28 @@ export default function Settings() {
                           </select>
                         </div>
                       </div>
+                      <div className="mt-4 grid gap-2 border-t border-border pt-4">
+                        <label htmlFor={`tracked-repo-agent-instructions-${id}`} className="text-label uppercase tracking-wider text-muted-foreground">
+                          Agent instructions
+                        </label>
+                        <textarea
+                          id={`tracked-repo-agent-instructions-${id}`}
+                          defaultValue={repo.agentInstructions}
+                          onBlur={(e) => {
+                            const next = e.currentTarget.value;
+                            if (next !== repo.agentInstructions) {
+                              updateRepoSettingsMutation.mutate({
+                                repo: repo.repo,
+                                agentInstructions: next,
+                              });
+                            }
+                          }}
+                          disabled={updateRepoSettingsMutation.isPending}
+                          rows={4}
+                          placeholder="Repository-specific instructions for issue work and PR babysitter runs."
+                          className="min-h-24 resize-y border border-border bg-transparent px-3 py-2 text-body leading-relaxed focus:border-primary focus:outline-none focus-visible:ring-1 focus-visible:ring-ring focus-visible:ring-offset-1 focus-visible:ring-offset-background disabled:opacity-50"
+                        />
+                      </div>
                     </div>
                   );
                 })}
diff --git a/docs/assets/PatchDeck-Settings.png b/docs/assets/PatchDeck-Settings.png
index 56bd128..b0bd5f0 100644
Binary files a/docs/assets/PatchDeck-Settings.png and b/docs/assets/PatchDeck-Settings.png differ
diff --git a/server/babysitter.test.ts b/server/babysitter.test.ts
index 206ac06..0e6570c 100644
--- a/server/babysitter.test.ts
+++ b/server/babysitter.test.ts
@@ -5023,6 +5023,9 @@ test("babysitPR retries docs assessment for same-SHA failed state", async () =>
 
 test("babysitPR runs agent for docs-only work when docs assessment says needed", async () => {
   const storage = new MemStorage();
+  await storage.updateRepoSettings("alex-morgan-o/lolodex", {
+    agentInstructions: "Use pnpm docs:check before finishing.",
+  });
   const pr = await storage.addPR({
     number: 106,
     title: "Docs-only remediation",
@@ -5092,6 +5095,7 @@ test("babysitPR runs agent for docs-only work when docs assessment says needed",
     assert.equal(updated?.docsAssessment?.status, "needed");
     assert.match(capturedPrompt, /Approved documentation tasks:/);
     assert.match(capturedPrompt, /README and API docs need updates/);
+    assert.match(capturedPrompt, /Use pnpm docs:check before finishing\./);
     assert.match(capturedPrompt, /DOCS_SUMMARY_START <changed\|no_change>/);
   } finally {
     delete process.env.CODEFACTORY_HOME;
diff --git a/server/babysitter.ts b/server/babysitter.ts
index b45a90c..4a8b343 100644
--- a/server/babysitter.ts
+++ b/server/babysitter.ts
@@ -390,14 +390,29 @@ function truncateForPrompt(input: string, maxChars: number): string {
   return `${input.slice(0, maxChars)}\n... (truncated)`;
 }
 
+function formatRepoAgentInstructions(instructions?: string | null): string[] {
+  const trimmed = instructions?.trim();
+  if (!trimmed) {
+    return ["Repository agent instructions: none"];
+  }
+
+  return [
+    "Repository agent instructions:",
+    "```",
+    truncateForPrompt(trimmed, 4000),
+    "```",
+  ];
+}
+
 function buildDocumentationAssessmentPrompt(params: {
   pr: PR;
   pullSummary: GitHubPullSummary;
   changedFiles: string;
   diffStat: string;
   diffPreview: string;
+  agentInstructions?: string | null;
 }): string {
-  const { pr, pullSummary, changedFiles, diffStat, diffPreview } = params;
+  const { pr, pullSummary, changedFiles, diffStat, diffPreview, agentInstructions } = params;
 
   return [
     "You are deciding whether a pull request requires repository documentation updates.",
@@ -408,6 +423,8 @@ function buildDocumentationAssessmentPrompt(params: {
     `Base branch: ${pullSummary.baseRef}`,
     `Head branch: ${pullSummary.headRef}`,
     "",
+    ...formatRepoAgentInstructions(agentInstructions),
+    "",
     "Changed files (git diff --name-only origin/base...HEAD):",
     truncateForPrompt(changedFiles || "None", 4000),
     "",
@@ -452,8 +469,9 @@ function buildConflictResolutionPrompt(params: {
   pullSummary: GitHubPullSummary;
   remoteName: string;
   conflictFiles: string[];
+  agentInstructions?: string | null;
 }): string {
-  const { pr, pullSummary, remoteName, conflictFiles } = params;
+  const { pr, pullSummary, remoteName, conflictFiles, agentInstructions } = params;
 
   return [
     `You are acting as an autonomous PR babysitter for ${pr.repo} PR #${pr.number}.`,
@@ -465,6 +483,8 @@ function buildConflictResolutionPrompt(params: {
     `Head remote: ${remoteName}`,
     "You are running inside an isolated app-owned worktree under ~/.patchdeck.",
     "",
+    ...formatRepoAgentInstructions(agentInstructions),
+    "",
     "A merge from the base branch into the head branch has been started but has conflicts.",
     "The following files have merge conflicts:",
     ...conflictFiles.map((f) => `  - ${f}`),
@@ -490,8 +510,9 @@ function buildAgentFixPrompt(params: {
   commentTasks: FeedbackItem[];
   statusTasks: { context: string; description: string; targetUrl: string | null }[];
   docsTaskSummary: string | null;
+  agentInstructions?: string | null;
 }): string {
-  const { pr, pullSummary, remoteName, commentTasks, statusTasks, docsTaskSummary } = params;
+  const { pr, pullSummary, remoteName, commentTasks, statusTasks, docsTaskSummary, agentInstructions } = params;
 
   const commentSection = commentTasks.length
     ? commentTasks
@@ -543,6 +564,8 @@ function buildAgentFixPrompt(params: {
     "GitHub follow-up replies and review-thread resolution will be handled by the babysitter after your run.",
     "If a task is invalid after inspection, explain it in your final response and include the exact audit token.",
     "",
+    ...formatRepoAgentInstructions(agentInstructions),
+    "",
     "Approved review-comment tasks:",
     commentSection,
     "",
@@ -571,8 +594,9 @@ function buildCodeOwnerFallbackPrompt(params: {
   pr: PR;
   pullSummary: GitHubPullSummary;
   remoteName: string;
+  agentInstructions?: string | null;
 }): string {
-  const { pr, pullSummary, remoteName } = params;
+  const { pr, pullSummary, remoteName, agentInstructions } = params;
 
   return [
     pr.url,
@@ -589,6 +613,8 @@ function buildCodeOwnerFallbackPrompt(params: {
     "- Review the latest PR review comments, unresolved review threads, issue comments, and failing checks.",
     "- Treat reviewer feedback as actionable by default, but validate it against the current code before changing anything. You can reject the feedback if it's not a valid feedback.",
     "",
+    ...formatRepoAgentInstructions(agentInstructions),
+    "",
     "Task:",
     "1. Fetch and inspect the current PR state.",
     "2. For each review comment/thread:",
@@ -3376,10 +3402,12 @@ export class PRBabysitter {
         });
         await ensureGitIdentity(worktreePath, this.runtime.runCommand);
 
+        const fallbackRepoSettings = await this.storage.getRepoSettings(pr.repo);
         const prompt = buildCodeOwnerFallbackPrompt({
           pr,
           pullSummary,
           remoteName,
+          agentInstructions: fallbackRepoSettings?.agentInstructions ?? "",
         });
 
         await updateRunRecord({
@@ -3559,6 +3587,8 @@ export class PRBabysitter {
       await updateRunRecord({
         resolvedAgent: agent,
       });
+      const repoSettings = await this.storage.getRepoSettings(pr.repo);
+      const repoAgentInstructions = repoSettings?.agentInstructions ?? "";
       const parsedRepo = parseRepoSlug(pr.repo);
 
       if (!parsedRepo) {
@@ -4479,6 +4509,7 @@ export class PRBabysitter {
                 changedFiles: changedFilesResult.stdout.trim(),
                 diffStat: diffStatResult.stdout.trim(),
                 diffPreview: diffPreviewResult.stdout.trim(),
+                agentInstructions: repoAgentInstructions,
               });
               await queueLog(pr.id, "info", `Evaluating documentation needs with ${agent}`, {
                 phase: "evaluate.docs",
@@ -4680,6 +4711,7 @@ export class PRBabysitter {
                 pullSummary,
                 remoteName,
                 conflictFiles: normalizedConflictFiles,
+                agentInstructions: repoAgentInstructions,
               });
 
               await queueLog(pr.id, "info", `Launching ${agent} to resolve merge conflicts`, {
@@ -4818,6 +4850,7 @@ export class PRBabysitter {
               commentTasks: effectiveCommentTasks,
               statusTasks,
               docsTaskSummary,
+              agentInstructions: repoAgentInstructions,
             });
 
             await updateRunRecord({
diff --git a/server/backgroundJobHandlers.test.ts b/server/backgroundJobHandlers.test.ts
index bba4c9d..fb31f82 100644
--- a/server/backgroundJobHandlers.test.ts
+++ b/server/backgroundJobHandlers.test.ts
@@ -317,6 +317,9 @@ test("work_issue handler opens a PR after a successful repair run", async () =>
     codingAgent: "claude",
     postGitHubProgressReplies: true,
   });
+  await storage.updateRepoSettings("acme/widgets", {
+    agentInstructions: "Use pnpm for this repository.",
+  });
   const queue = new BackgroundJobQueue(storage);
   const job = await queue.enqueue(
     "work_issue",
@@ -332,7 +335,7 @@ test("work_issue handler opens a PR after a successful repair run", async () =>
   );
   const pullsCreated: Array<Record<string, unknown>> = [];
   const commentsCreated: Array<Record<string, unknown>> = [];
-  const repairCalls: Array<{ repo: string; issueNumber: number; baseBranch: string; repoCloneUrl: string }> = [];
+  const repairCalls: Array<{ repo: string; issueNumber: number; baseBranch: string; repoCloneUrl: string; agentInstructions?: string | null }> = [];
   const octokit = {
     issues: {
       get: async () => ({
@@ -375,6 +378,7 @@ test("work_issue handler opens a PR after a successful repair run", async () =>
           issueNumber: input.issueNumber,
           baseBranch: input.baseBranch,
           repoCloneUrl: input.repoCloneUrl,
+          agentInstructions: input.agentInstructions,
         });
         return {
           accepted: true,
@@ -394,6 +398,7 @@ test("work_issue handler opens a PR after a successful repair run", async () =>
     issueNumber: 17,
     baseBranch: "main",
     repoCloneUrl: "https://x-access-token:gho_token@github.com/acme/widgets.git",
+    agentInstructions: "Use pnpm for this repository.",
   }]);
   assert.equal(pullsCreated.length, 1);
   assert.equal(pullsCreated[0]?.head, "issue/17-fix-the-toggle-123");
diff --git a/server/backgroundJobHandlers.ts b/server/backgroundJobHandlers.ts
index b5154bd..1918501 100644
--- a/server/backgroundJobHandlers.ts
+++ b/server/backgroundJobHandlers.ts
@@ -577,6 +577,7 @@ export function createBackgroundJobHandlers(params: {
           repoCloneUrl: buildGitHubCloneUrl(issue.repoFullName, githubToken),
           agent,
           agentSettings,
+          agentInstructions: repoSettings?.agentInstructions ?? "",
           subtasks: subtasks.length >= 2 ? subtasks : undefined,
         });
       } catch (error) {
diff --git a/server/issueWorkAgent.test.ts b/server/issueWorkAgent.test.ts
index 267a083..2daa757 100644
--- a/server/issueWorkAgent.test.ts
+++ b/server/issueWorkAgent.test.ts
@@ -40,6 +40,24 @@ test("buildIssueWorkPrompt includes repository contribution guidance when presen
   assert.match(prompt, /Keep changes small and update tests\./);
 });
 
+test("buildIssueWorkPrompt includes custom repository agent instructions", () => {
+  const prompt = buildIssueWorkPrompt({
+    repo: "acme/widgets",
+    issueNumber: 17,
+    issueTitle: "Fix the toggle",
+    issueUrl: "https://github.com/acme/widgets/issues/17",
+    issueBody: "The toggle is stuck",
+    labels: [],
+    author: "alice",
+    baseBranch: "main",
+    agent: "claude",
+    agentInstructions: "Use pnpm test for focused verification.",
+  });
+
+  assert.match(prompt, /Repository agent instructions:/);
+  assert.match(prompt, /Use pnpm test for focused verification\./);
+});
+
 test("runIssueWorkRepair commits, pushes, and verifies the issue branch", async () => {
   const calls: Array<{ command: string; args: string[]; cwd?: string }> = [];
   let agentPrompt = "";
diff --git a/server/issueWorkAgent.ts b/server/issueWorkAgent.ts
index 5cab862..4bf4ed5 100644
--- a/server/issueWorkAgent.ts
+++ b/server/issueWorkAgent.ts
@@ -20,6 +20,7 @@ export type IssueWorkPromptInput = {
   agent: CodingAgent;
   agentSettings?: AgentRuntimeSettings;
   contributionGuidance?: string | null;
+  agentInstructions?: string | null;
   subtasks?: IssueSubtask[];
 };
 
@@ -77,6 +78,7 @@ export function buildIssueWorkPrompt(input: IssueWorkPromptInput): string {
   const labels = input.labels.length > 0 ? input.labels.join(", ") : "none";
   const author = input.author || "unknown";
   const contributionGuidance = input.contributionGuidance?.trim();
+  const agentInstructions = input.agentInstructions?.trim();
   const guidance = contributionGuidance
     ? [
         "Repository contribution guidance:",
@@ -89,6 +91,14 @@ export function buildIssueWorkPrompt(input: IssueWorkPromptInput): string {
         "- No CONTRIBUTING.md was found in the repository.",
         "- Use the concise issue-reply and PR-body templates below.",
       ].join("\n");
+  const customInstructions = agentInstructions
+    ? [
+        "Repository agent instructions:",
+        "```",
+        trimText(agentInstructions, 4000),
+        "```",
+      ].join("\n")
+    : "Repository agent instructions: none";
 
   const hasSubtasks = (input.subtasks?.length ?? 0) >= 2;
   const subtaskSection = hasSubtasks
@@ -145,6 +155,8 @@ export function buildIssueWorkPrompt(input: IssueWorkPromptInput): string {
     "",
     guidance,
     "",
+    customInstructions,
+    "",
     "Fallback response template:",
     "```",
     "## Summary",
@@ -448,6 +460,7 @@ export async function runIssueWorkRepair(
         repoContributionGuidance ? `CONTRIBUTING.md:\n${repoContributionGuidance}` : null,
         repoPullRequestTemplate ? `.github/pull_request_template.md:\n${repoPullRequestTemplate}` : null,
       ].filter((value): value is string => Boolean(value)).join("\n\n") || null,
+      agentInstructions: input.agentInstructions,
     });
     const branchCreate = await deps.runCommand(
       "git",
diff --git a/server/memoryStorage.test.ts b/server/memoryStorage.test.ts
index 081c761..5a4a845 100644
--- a/server/memoryStorage.test.ts
+++ b/server/memoryStorage.test.ts
@@ -493,6 +493,7 @@ describe("MemStorage", () => {
         codexReasoningEffort: null,
         claudeModel: null,
         claudeEffort: null,
+        agentInstructions: "",
       }]);
     });
 
@@ -516,6 +517,7 @@ describe("MemStorage", () => {
         codexReasoningEffort: null,
         claudeModel: null,
         claudeEffort: null,
+        agentInstructions: "",
       });
 
       const config = await storage.getConfig();
@@ -534,6 +536,7 @@ describe("MemStorage", () => {
         codexReasoningEffort: null,
         claudeModel: null,
         claudeEffort: null,
+        agentInstructions: "",
       });
     });
   });
diff --git a/server/memoryStorage.ts b/server/memoryStorage.ts
index 96b9ede..0298caf 100644
--- a/server/memoryStorage.ts
+++ b/server/memoryStorage.ts
@@ -300,6 +300,7 @@ export class MemStorage implements IStorage {
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     };
     const next = applyWatchedRepoUpdate(existing, updates);
     this.repoSettings.set(repo, next);
@@ -453,6 +454,7 @@ export class MemStorage implements IStorage {
           codexReasoningEffort: null,
           claudeModel: null,
           claudeEffort: null,
+          agentInstructions: "",
         });
       }
     }
diff --git a/server/routes.test.ts b/server/routes.test.ts
index b9e4d1f..3832ed5 100644
--- a/server/routes.test.ts
+++ b/server/routes.test.ts
@@ -1352,6 +1352,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
       codexReasoningEffort: "default" | "low" | "medium" | "high" | "xhigh" | null;
       claudeModel: string | null;
       claudeEffort: "default" | "low" | "medium" | "high" | "xhigh" | "max" | null;
+      agentInstructions: string;
     }>;
     assert.deepEqual(initial, [{
       repo: "acme/widgets",
@@ -1365,6 +1366,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     }]);
 
     const updateResponse = await fetch(`${harness.baseUrl}/api/repos/settings`, {
@@ -1382,6 +1384,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
         codexReasoningEffort: "high",
         claudeModel: "sonnet",
         claudeEffort: "xhigh",
+        agentInstructions: "Prefer the repo's pnpm scripts before npm.",
       }),
     });
     assert.equal(updateResponse.status, 200);
@@ -1397,6 +1400,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
       codexReasoningEffort: "default" | "low" | "medium" | "high" | "xhigh" | null;
       claudeModel: string | null;
       claudeEffort: "default" | "low" | "medium" | "high" | "xhigh" | "max" | null;
+      agentInstructions: string;
     };
     // Enabling auto-work implicitly enables auto-evaluate — they're dependent settings,
     // not independent flags. Verifies coercion in applyWatchedRepoUpdate.
@@ -1412,6 +1416,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
       codexReasoningEffort: "high",
       claudeModel: "sonnet",
       claudeEffort: "xhigh",
+      agentInstructions: "Prefer the repo's pnpm scripts before npm.",
     });
 
     const persisted = await harness.storage.getRepoSettings("acme/widgets");
@@ -1427,6 +1432,7 @@ test("GET/PATCH /api/repos/settings exposes repo-level settings", async () => {
       codexReasoningEffort: "high",
       claudeModel: "sonnet",
       claudeEffort: "xhigh",
+      agentInstructions: "Prefer the repo's pnpm scripts before npm.",
     });
   } finally {
     await harness.close();
@@ -1465,6 +1471,7 @@ test("PATCH /api/repos/settings can update only ownPrsOnly", async () => {
       codexReasoningEffort: "default" | "low" | "medium" | "high" | "xhigh" | null;
       claudeModel: string | null;
       claudeEffort: "default" | "low" | "medium" | "high" | "xhigh" | "max" | null;
+      agentInstructions: string;
     };
     assert.deepEqual(updated, {
       repo: "acme/widgets",
@@ -1478,6 +1485,7 @@ test("PATCH /api/repos/settings can update only ownPrsOnly", async () => {
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     });
   } finally {
     await harness.close();
diff --git a/server/routes.ts b/server/routes.ts
index 753c204..3df62e5 100644
--- a/server/routes.ts
+++ b/server/routes.ts
@@ -429,6 +429,7 @@ export async function registerRoutes(
         codexReasoningEffort: codexReasoningEffortSchema.nullable().optional(),
         claudeModel: z.string().nullable().optional(),
         claudeEffort: claudeEffortSchema.nullable().optional(),
+        agentInstructions: z.string().optional(),
       }).refine(
         (value) => (
           value.autoCreateReleases !== undefined
@@ -441,6 +442,7 @@ export async function registerRoutes(
           || value.codexReasoningEffort !== undefined
           || value.claudeModel !== undefined
           || value.claudeEffort !== undefined
+          || value.agentInstructions !== undefined
         ),
         "At least one repository setting must be provided",
       ).parse(req.body);
diff --git a/server/sqliteStorage.ts b/server/sqliteStorage.ts
index e5e6f97..46af77c 100644
--- a/server/sqliteStorage.ts
+++ b/server/sqliteStorage.ts
@@ -183,6 +183,7 @@ type WatchedRepoRow = {
   codex_reasoning_effort: Config["codexReasoningEffort"] | null;
   claude_model: string | null;
   claude_effort: Config["claudeEffort"] | null;
+  agent_instructions: string | null;
 };
 
 type FeedbackItemRow = {
@@ -604,7 +605,8 @@ export class SqliteStorage implements IStorage {
         codex_model TEXT,
         codex_reasoning_effort TEXT,
         claude_model TEXT,
-        claude_effort TEXT
+        claude_effort TEXT,
+        agent_instructions TEXT NOT NULL DEFAULT ''
       );
 
       CREATE TABLE IF NOT EXISTS prs (
@@ -969,6 +971,7 @@ export class SqliteStorage implements IStorage {
     this.ensureColumn("watched_repos", "codex_reasoning_effort", "TEXT");
     this.ensureColumn("watched_repos", "claude_model", "TEXT");
     this.ensureColumn("watched_repos", "claude_effort", "TEXT");
+    this.ensureColumn("watched_repos", "agent_instructions", "TEXT NOT NULL DEFAULT ''");
     this.exec("UPDATE watched_repos SET issue_auto_evaluate = 1 WHERE issue_auto_work = 1 AND issue_auto_evaluate = 0");
     this.ensureColumn("config", "max_concurrent_issue_evaluations", "INTEGER NOT NULL DEFAULT 2");
     this.ensureColumn("config", "max_concurrent_issue_work", "INTEGER NOT NULL DEFAULT 1");
@@ -1239,7 +1242,7 @@ export class SqliteStorage implements IStorage {
       for (const repo of config.watchedRepos) {
         const settings = watchedRepoSettings.get(repo);
         this.run(
-          "INSERT INTO watched_repos (repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
+          "INSERT INTO watched_repos (repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort, agent_instructions) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
           repo,
           settings?.auto_create_releases ?? 0,
           settings?.own_prs_only ?? 1,
@@ -1251,6 +1254,7 @@ export class SqliteStorage implements IStorage {
           settings?.codex_reasoning_effort ?? null,
           settings?.claude_model ?? null,
           settings?.claude_effort ?? null,
+          settings?.agent_instructions ?? "",
         );
       }
     });
@@ -1269,12 +1273,13 @@ export class SqliteStorage implements IStorage {
       codexReasoningEffort: row.codex_reasoning_effort ?? null,
       claudeModel: row.claude_model ?? null,
       claudeEffort: row.claude_effort ?? null,
+      agentInstructions: row.agent_instructions ?? "",
     };
   }
 
   private getWatchedRepoRows(): WatchedRepoRow[] {
     return this.all<WatchedRepoRow>(
-      "SELECT repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort FROM watched_repos ORDER BY repo ASC",
+      "SELECT repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort, agent_instructions FROM watched_repos ORDER BY repo ASC",
     );
   }
 
@@ -2057,7 +2062,7 @@ export class SqliteStorage implements IStorage {
 
   async getRepoSettings(repo: string): Promise<WatchedRepo | undefined> {
     const row = this.get<WatchedRepoRow>(
-      "SELECT repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort FROM watched_repos WHERE repo = ?",
+      "SELECT repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort, agent_instructions FROM watched_repos WHERE repo = ?",
       repo,
     );
     return row ? this.parseWatchedRepoRow(row) : undefined;
@@ -2079,14 +2084,15 @@ export class SqliteStorage implements IStorage {
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     };
     const next = applyWatchedRepoUpdate(existing, updates);
 
     this.withWriteTransaction(() => {
       this.run(
         `
-          INSERT INTO watched_repos (repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort)
-          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+          INSERT INTO watched_repos (repo, auto_create_releases, own_prs_only, issue_auto_evaluate, issue_auto_work, pr_auto_monitor, coding_agent_override, codex_model, codex_reasoning_effort, claude_model, claude_effort, agent_instructions)
+          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
           ON CONFLICT(repo) DO UPDATE SET
             auto_create_releases = excluded.auto_create_releases,
             own_prs_only = excluded.own_prs_only,
@@ -2097,7 +2103,8 @@ export class SqliteStorage implements IStorage {
             codex_model = excluded.codex_model,
             codex_reasoning_effort = excluded.codex_reasoning_effort,
             claude_model = excluded.claude_model,
-            claude_effort = excluded.claude_effort
+            claude_effort = excluded.claude_effort,
+            agent_instructions = excluded.agent_instructions
         `,
         next.repo,
         Number(next.autoCreateReleases),
@@ -2110,6 +2117,7 @@ export class SqliteStorage implements IStorage {
         next.codexReasoningEffort,
         next.claudeModel,
         next.claudeEffort,
+        next.agentInstructions,
       );
     });
 
diff --git a/server/storage.test.ts b/server/storage.test.ts
index 2678a87..655ae6c 100644
--- a/server/storage.test.ts
+++ b/server/storage.test.ts
@@ -254,6 +254,7 @@ test("SqliteStorage reloads config and PR state from the same root", async () =>
     codexReasoningEffort: "medium",
     claudeModel: null,
     claudeEffort: null,
+    agentInstructions: "",
   });
   assert.equal(runtime.drainMode, true);
   assert.equal(runtime.drainRequestedAt, "2026-03-18T10:00:00.000Z");
@@ -478,6 +479,10 @@ test("SqliteStorage schema defaults automatic release creation off", async () =>
       watchedRepoColumns.find((column) => column.name === "issue_auto_work")?.dflt_value,
       "0",
     );
+    assert.equal(
+      watchedRepoColumns.find((column) => column.name === "agent_instructions")?.dflt_value,
+      "''",
+    );
   } finally {
     db.close();
     storage.close();
@@ -528,6 +533,7 @@ test("SqliteStorage updateRepoSettings tracks a previously untracked repo", asyn
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     });
 
     const after = await storage.getConfig();
@@ -546,6 +552,7 @@ test("SqliteStorage updateRepoSettings tracks a previously untracked repo", asyn
       codexReasoningEffort: null,
       claudeModel: null,
       claudeEffort: null,
+      agentInstructions: "",
     });
   } finally {
     storage.close();
diff --git a/shared/models.ts b/shared/models.ts
index 296bcc6..363a50e 100644
--- a/shared/models.ts
+++ b/shared/models.ts
@@ -423,10 +423,14 @@ export function applyWatchedRepoUpdate(
   existing: WatchedRepo,
   updates: Partial<Omit<WatchedRepo, "repo">>,
 ): WatchedRepo {
+  const agentInstructions = updates.agentInstructions === undefined
+    ? existing.agentInstructions
+    : updates.agentInstructions.trim();
   const merged = {
     ...existing,
     ...updates,
     repo: existing.repo,
+    agentInstructions,
   };
   if (merged.issueAutoWork) {
     merged.issueAutoEvaluate = true;
diff --git a/shared/schema.ts b/shared/schema.ts
index 88a8334..2fffb37 100644
--- a/shared/schema.ts
+++ b/shared/schema.ts
@@ -750,6 +750,7 @@ export const watchedRepoSchema = z.object({
   codexReasoningEffort: codexReasoningEffortSchema.nullable(),
   claudeModel: z.string().nullable(),
   claudeEffort: claudeEffortSchema.nullable(),
+  agentInstructions: z.string().default(""),
 });
 export type WatchedRepo = z.infer<typeof watchedRepoSchema>;