diff --git a/apps/server/src/sourceControl/GitHubCli.test.ts b/apps/server/src/sourceControl/GitHubCli.test.ts
index 5df4862b409..f96d18e3a33 100644
--- a/apps/server/src/sourceControl/GitHubCli.test.ts
+++ b/apps/server/src/sourceControl/GitHubCli.test.ts
@@ -210,18 +210,20 @@ describe("GitHubCli.layer", () => {
 
   it.effect("reads repository clone URLs", () =>
     Effect.gen(function* () {
-      mockRun.mockReturnValueOnce(
-        Effect.succeed(
-          processOutput(
-            // @effect-diagnostics-next-line preferSchemaOverJson:off
-            JSON.stringify({
-              nameWithOwner: "octocat/codething-mvp",
-              url: "https://github.com/octocat/codething-mvp",
-              sshUrl: "git@github.com:octocat/codething-mvp.git",
-            }),
+      mockRun
+        .mockReturnValueOnce(
+          Effect.succeed(
+            processOutput(
+              // @effect-diagnostics-next-line preferSchemaOverJson:off
+              JSON.stringify({
+                nameWithOwner: "octocat/codething-mvp",
+                url: "https://github.com/octocat/codething-mvp",
+                sshUrl: "git@github.com:octocat/codething-mvp.git",
+              }),
+            ),
           ),
-        ),
-      );
+        )
+        .mockReturnValueOnce(Effect.succeed(processOutput("https\n")));
 
       const gh = yield* GitHubCli.GitHubCli;
       const result = yield* gh.getRepositoryCloneUrls({
@@ -233,6 +235,14 @@ describe("GitHubCli.layer", () => {
         nameWithOwner: "octocat/codething-mvp",
         url: "https://github.com/octocat/codething-mvp",
         sshUrl: "git@github.com:octocat/codething-mvp.git",
+        preferredProtocol: "https",
+      });
+      expect(mockRun).toHaveBeenNthCalledWith(2, {
+        operation: "GitHubCli.execute",
+        command: "gh",
+        args: ["config", "get", "git_protocol", "--host", "github.com"],
+        cwd: "/repo",
+        timeoutMs: 30_000,
       });
     }).pipe(Effect.provide(layer)),
   );
diff --git a/apps/server/src/sourceControl/GitHubCli.ts b/apps/server/src/sourceControl/GitHubCli.ts
index bf3f27378b5..17d4da82540 100644
--- a/apps/server/src/sourceControl/GitHubCli.ts
+++ b/apps/server/src/sourceControl/GitHubCli.ts
@@ -194,6 +194,7 @@ export interface GitHubRepositoryCloneUrls {
   readonly nameWithOwner: string;
   readonly url: string;
   readonly sshUrl: string;
+  readonly preferredProtocol?: "ssh" | "https";
 }
 
 export class GitHubCli extends Context.Service<
@@ -266,6 +267,22 @@ function normalizeRepositoryCloneUrls(
   };
 }
 
+function repositoryHost(url: string): string {
+  try {
+    return new URL(url).hostname;
+  } catch {
+    return "github.com";
+  }
+}
+
+function parseConfiguredGitProtocol(stdout: string): "ssh" | "https" | undefined {
+  const protocol = stdout.trim().toLowerCase();
+  if (protocol === "ssh" || protocol === "https") {
+    return protocol;
+  }
+  return undefined;
+}
+
 /**
  * `gh repo create` prints the canonical URL of the new repository on stdout
  * (e.g. `https://github.com/owner/repo`). Reading it back here avoids a
@@ -409,6 +426,20 @@ export const make = Effect.gen(function* () {
           ),
         ),
         Effect.map(normalizeRepositoryCloneUrls),
+        Effect.flatMap((urls) =>
+          execute({
+            cwd: input.cwd,
+            args: ["config", "get", "git_protocol", "--host", repositoryHost(urls.url)],
+          }).pipe(
+            Effect.map((result) => parseConfiguredGitProtocol(result.stdout)),
+            Effect.map((preferredProtocol) =>
+              preferredProtocol === undefined ? urls : { ...urls, preferredProtocol },
+            ),
+            // Repository lookup should still work when older `gh` versions or
+            // incomplete host configuration cannot report a preference.
+            Effect.orElseSucceed(() => urls),
+          ),
+        ),
       ),
     createRepository: (input) =>
       execute({
diff --git a/apps/server/src/sourceControl/SourceControlRepositoryService.test.ts b/apps/server/src/sourceControl/SourceControlRepositoryService.test.ts
index 861da9a10e0..0aea0942680 100644
--- a/apps/server/src/sourceControl/SourceControlRepositoryService.test.ts
+++ b/apps/server/src/sourceControl/SourceControlRepositoryService.test.ts
@@ -150,7 +150,7 @@ it.effect("preserves provider failures without deriving the repository message f
   }).pipe(Effect.provide(makeLayer({ provider })));
 });
 
-it.effect("clones a looked-up repository into the requested destination", () =>
+it.effect("clones a looked-up repository using the provider's HTTPS preference", () =>
   Effect.gen(function* () {
     const fs = yield* FileSystem.FileSystem;
     const parent = yield* fs.makeTempDirectoryScoped({
@@ -158,6 +158,10 @@ it.effect("clones a looked-up repository into the requested destination", () =>
     });
     const destinationPath = `${parent}/t3code`;
     const cloneCalls: Array<{ cwd: string; args: ReadonlyArray<string> }> = [];
+    const provider = makeProvider({
+      getRepositoryCloneUrls: () =>
+        Effect.succeed({ ...CLONE_URLS, preferredProtocol: "https" as const }),
+    });
 
     yield* Effect.gen(function* () {
       const service = yield* SourceControlRepositoryService.SourceControlRepositoryService;
@@ -165,14 +169,58 @@ it.effect("clones a looked-up repository into the requested destination", () =>
         provider: "github",
         repository: "octocat/t3code",
         destinationPath,
-        protocol: "https",
       });
 
       assert.deepStrictEqual(result, {
         cwd: destinationPath,
         remoteUrl: CLONE_URLS.url,
-        repository: { provider: "github", ...CLONE_URLS },
+        repository: {
+          provider: "github",
+          ...CLONE_URLS,
+          preferredProtocol: "https",
+        },
+      });
+      assert.deepStrictEqual(cloneCalls, [
+        {
+          cwd: parent,
+          args: ["clone", CLONE_URLS.url, "t3code"],
+        },
+      ]);
+    }).pipe(
+      Effect.provide(
+        makeLayer({
+          provider,
+          git: {
+            execute: (input) =>
+              Effect.sync(() => {
+                cloneCalls.push({ cwd: input.cwd, args: input.args });
+                return processOutput();
+              }),
+          },
+        }),
+      ),
+    );
+  }).pipe(Effect.provide(NodeServices.layer)),
+);
+
+it.effect("uses HTTPS as the automatic fallback without a provider preference", () =>
+  Effect.gen(function* () {
+    const fs = yield* FileSystem.FileSystem;
+    const parent = yield* fs.makeTempDirectoryScoped({
+      prefix: "t3-source-control-clone-parent-",
+    });
+    const destinationPath = `${parent}/t3code`;
+    const cloneCalls: Array<{ cwd: string; args: ReadonlyArray<string> }> = [];
+
+    yield* Effect.gen(function* () {
+      const service = yield* SourceControlRepositoryService.SourceControlRepositoryService;
+      const result = yield* service.cloneRepository({
+        provider: "github",
+        repository: "octocat/t3code",
+        destinationPath,
       });
+
+      assert.strictEqual(result.remoteUrl, CLONE_URLS.url);
       assert.deepStrictEqual(cloneCalls, [
         {
           cwd: parent,
diff --git a/apps/server/src/sourceControl/SourceControlRepositoryService.ts b/apps/server/src/sourceControl/SourceControlRepositoryService.ts
index 1b46369e25c..cd2426d4762 100644
--- a/apps/server/src/sourceControl/SourceControlRepositoryService.ts
+++ b/apps/server/src/sourceControl/SourceControlRepositoryService.ts
@@ -61,6 +61,7 @@ function toRepositoryInfo(
     nameWithOwner: urls.nameWithOwner,
     url: urls.url,
     sshUrl: urls.sshUrl,
+    ...(urls.preferredProtocol ? { preferredProtocol: urls.preferredProtocol } : {}),
   };
 }
 
@@ -71,8 +72,9 @@ function selectRemoteUrl(
   switch (protocol ?? "auto") {
     case "https":
       return urls.url;
-    case "ssh":
     case "auto":
+      return urls.preferredProtocol === "ssh" ? urls.sshUrl : urls.url;
+    case "ssh":
       return urls.sshUrl;
   }
 }
diff --git a/apps/web/src/components/CommandPalette.logic.test.ts b/apps/web/src/components/CommandPalette.logic.test.ts
index 651fe34e4b4..f638e79a211 100644
--- a/apps/web/src/components/CommandPalette.logic.test.ts
+++ b/apps/web/src/components/CommandPalette.logic.test.ts
@@ -4,6 +4,7 @@ import type { Thread } from "../types";
 import {
   buildThreadActionItems,
   filterCommandPaletteGroups,
+  getCloneSourceInput,
   type CommandPaletteGroup,
 } from "./CommandPalette.logic";
 
@@ -35,6 +36,26 @@ function makeThread(overrides: Partial<Thread> = {}): Thread {
   };
 }
 
+it("uses provider-based automatic selection for looked-up repositories", () => {
+  expect(
+    getCloneSourceInput({
+      repository: {
+        provider: "github",
+        nameWithOwner: "octocat/t3code",
+        url: "https://github.com/octocat/t3code",
+        sshUrl: "git@github.com:octocat/t3code.git",
+      },
+      remoteUrl: "https://github.com/octocat/t3code",
+    }),
+  ).toEqual({ provider: "github", repository: "octocat/t3code", protocol: "auto" });
+});
+
+it("passes explicit clone URLs through unchanged", () => {
+  expect(
+    getCloneSourceInput({ repository: null, remoteUrl: "git@example.com:org/repo.git" }),
+  ).toEqual({ remoteUrl: "git@example.com:org/repo.git" });
+});
+
 describe("buildThreadActionItems", () => {
   it("orders threads by most recent activity and formats timestamps from updatedAt", () => {
     vi.useFakeTimers();
diff --git a/apps/web/src/components/CommandPalette.logic.ts b/apps/web/src/components/CommandPalette.logic.ts
index ab53adbefb1..e7a0c5c14e8 100644
--- a/apps/web/src/components/CommandPalette.logic.ts
+++ b/apps/web/src/components/CommandPalette.logic.ts
@@ -1,4 +1,9 @@
-import { type KeybindingCommand, type FilesystemBrowseEntry } from "@t3tools/contracts";
+import {
+  type FilesystemBrowseEntry,
+  type KeybindingCommand,
+  type SourceControlCloneRepositoryInput,
+  type SourceControlRepositoryInfo,
+} from "@t3tools/contracts";
 import type { SidebarThreadSortOrder } from "@t3tools/contracts/settings";
 import * as Arr from "effect/Array";
 import * as Result from "effect/Result";
@@ -54,6 +59,21 @@ export interface CommandPaletteView {
 
 export type CommandPaletteMode = "root" | "root-browse" | "submenu" | "submenu-browse";
 
+export function getCloneSourceInput(input: {
+  repository: SourceControlRepositoryInfo | null;
+  remoteUrl: string;
+}): Pick<SourceControlCloneRepositoryInput, "provider" | "repository" | "remoteUrl" | "protocol"> {
+  if (input.repository) {
+    return {
+      provider: input.repository.provider,
+      repository: input.repository.nameWithOwner,
+      protocol: "auto",
+    };
+  }
+
+  return { remoteUrl: input.remoteUrl };
+}
+
 export function filterBrowseEntries(input: {
   browseEntries: ReadonlyArray<FilesystemBrowseEntry>;
   browseFilterQuery: string;
diff --git a/apps/web/src/components/CommandPalette.tsx b/apps/web/src/components/CommandPalette.tsx
index 8dccf984457..f3098c8ef40 100644
--- a/apps/web/src/components/CommandPalette.tsx
+++ b/apps/web/src/components/CommandPalette.tsx
@@ -102,6 +102,7 @@ import {
   filterBrowseEntries,
   filterCommandPaletteGroups,
   getCommandPaletteInputPlaceholder,
+  getCloneSourceInput,
   getCommandPaletteMode,
   ITEM_ICON_CLASS,
   RECENT_THREAD_LIMIT,
@@ -1282,7 +1283,7 @@ function OpenCommandPaletteDialog(props: {
         source: addProjectCloneFlow.source,
         repositoryInput: rawRepository,
         repository,
-        remoteUrl: repository.sshUrl,
+        remoteUrl: repository.url,
       });
       setHighlightedItemValue(null);
       setQuery(destinationPath);
@@ -1329,7 +1330,7 @@ function OpenCommandPaletteDialog(props: {
     const cloneResult = await cloneRepository({
       environmentId: addProjectCloneFlow.environmentId,
       input: {
-        remoteUrl: addProjectCloneFlow.remoteUrl,
+        ...getCloneSourceInput(addProjectCloneFlow),
         destinationPath,
       },
     });
diff --git a/packages/contracts/src/sourceControl.ts b/packages/contracts/src/sourceControl.ts
index 104aadd9161..a0f64342960 100644
--- a/packages/contracts/src/sourceControl.ts
+++ b/packages/contracts/src/sourceControl.ts
@@ -40,6 +40,7 @@ export const SourceControlRepositoryCloneUrls = Schema.Struct({
   nameWithOwner: TrimmedNonEmptyString,
   url: TrimmedNonEmptyString,
   sshUrl: TrimmedNonEmptyString,
+  preferredProtocol: Schema.optional(Schema.Literals(["ssh", "https"])),
 });
 export type SourceControlRepositoryCloneUrls = typeof SourceControlRepositoryCloneUrls.Type;
 
@@ -54,6 +55,7 @@ export const SourceControlRepositoryInfo = Schema.Struct({
   nameWithOwner: TrimmedNonEmptyString,
   url: TrimmedNonEmptyString,
   sshUrl: TrimmedNonEmptyString,
+  preferredProtocol: Schema.optional(Schema.Literals(["ssh", "https"])),
 });
 export type SourceControlRepositoryInfo = typeof SourceControlRepositoryInfo.Type;