diff --git a/packages/cli/src/commands/render.ts b/packages/cli/src/commands/render.ts
index a07e1c988..d2049eb8b 100644
--- a/packages/cli/src/commands/render.ts
+++ b/packages/cli/src/commands/render.ts
@@ -57,6 +57,7 @@ import { formatLintFindings } from "../utils/lintFormat.js";
 import { loadProducer } from "../utils/producer.js";
 import { c } from "../ui/colors.js";
 import { formatBytes, formatRenderSummaryDetail, errorBox } from "../ui/format.js";
+import { warnIfWebmAlphaDropped } from "../utils/webmAlphaCheck.js";
 import { renderProgress } from "../ui/progress.js";
 import {
   trackRenderComplete,
@@ -1373,6 +1374,7 @@ async function renderDocker(
   // threaded back here; the summary shows render time only (never a wrong video
   // length). Probe the output with ffprobe if a duration figure is wanted here.
   printRenderComplete(outputPath, elapsed, options.quiet);
+  warnIfWebmAlphaDropped(outputPath, options.format, options.quiet);
   if (options.exitAfterComplete) scheduleRenderProcessExit();
   return { renderTimeMs: elapsed };
 }
@@ -1475,6 +1477,7 @@ export async function renderLocal(
     job.perfSummary?.compositionDurationSeconds,
     job.perfSummary?.totalFrames,
   );
+  warnIfWebmAlphaDropped(outputPath, options.format, options.quiet);
   if (!options.skipFeedback) {
     await maybePromptRenderFeedback({
       renderDurationMs: elapsed,
diff --git a/packages/cli/src/utils/webmAlphaCheck.test.ts b/packages/cli/src/utils/webmAlphaCheck.test.ts
new file mode 100644
index 000000000..7fc812ff0
--- /dev/null
+++ b/packages/cli/src/utils/webmAlphaCheck.test.ts
@@ -0,0 +1,29 @@
+import { describe, expect, it } from "vitest";
+import { webmAlphaAdvisory } from "./webmAlphaCheck.js";
+
+describe("webmAlphaAdvisory", () => {
+  it("warns when a probed webm lacks the ALPHA_MODE sidecar tag", () => {
+    // A build that dropped the alpha sidecar: ffprobe reported a stream but no
+    // ALPHA_MODE=1 tag. (pix_fmt is irrelevant — libvpx-vp9 always reports
+    // yuv420p; the sidecar tag is the real signal.)
+    const msg = webmAlphaAdvisory("webm", { probed: true, alphaMode: false });
+    expect(msg).toBeDefined();
+    expect(msg).toContain("ALPHA_MODE");
+    expect(msg).toContain("--format mov");
+  });
+
+  it("stays SILENT when the webm carries ALPHA_MODE=1 (working transparent WebM)", () => {
+    // Regression guard for the #2044 R1 blocker: a correct transparent WebM
+    // reports pix_fmt=yuv420p BUT ALPHA_MODE=1 — it must NOT warn.
+    expect(webmAlphaAdvisory("webm", { probed: true, alphaMode: true })).toBeUndefined();
+  });
+
+  it("stays silent when the output could not be probed", () => {
+    expect(webmAlphaAdvisory("webm", { probed: false, alphaMode: false })).toBeUndefined();
+  });
+
+  it("stays silent for non-webm formats (mp4 opaque; mov carries alpha natively)", () => {
+    expect(webmAlphaAdvisory("mp4", { probed: true, alphaMode: false })).toBeUndefined();
+    expect(webmAlphaAdvisory("mov", { probed: true, alphaMode: false })).toBeUndefined();
+  });
+});
diff --git a/packages/cli/src/utils/webmAlphaCheck.ts b/packages/cli/src/utils/webmAlphaCheck.ts
new file mode 100644
index 000000000..af1074c54
--- /dev/null
+++ b/packages/cli/src/utils/webmAlphaCheck.ts
@@ -0,0 +1,101 @@
+import { execFileSync } from "node:child_process";
+import { findFFprobe } from "../browser/ffmpeg.js";
+import { c } from "../ui/colors.js";
+
+/**
+ * Result of probing a WebM's first video stream for its alpha sidecar.
+ * `probed` distinguishes "ffprobe ran and reported a video stream" from a
+ * failed/absent probe (so a probe failure stays silent, not a false warning).
+ */
+export interface WebmAlphaProbe {
+  probed: boolean;
+  /** True when the VP9 stream declares the alpha sidecar (ALPHA_MODE=1 tag). */
+  alphaMode: boolean;
+}
+
+/**
+ * Decide whether to warn that a WebM render lost its transparency, or
+ * `undefined` when nothing is wrong / can't be determined.
+ *
+ * IMPORTANT — the signal is the `ALPHA_MODE=1` stream tag, NOT `pix_fmt`.
+ * libvpx-vp9 stores the alpha plane in a Matroska BlockAdditional sidecar and
+ * ALWAYS reports `pix_fmt=yuv420p` even for a correct transparent WebM (see
+ * docs/guides/rendering.mdx and the webm-concat-copy smoke test). A working
+ * encode writes `ALPHA_MODE=1`; an ffmpeg/libvpx build that can't emit the
+ * sidecar omits the tag and produces genuinely opaque output. Keying on the
+ * tag means builds that preserve alpha stay silent (no false positive) and
+ * only builds that actually drop it get the warning.
+ *
+ * Pure over (format, probe) so the decision is unit-testable without spawning
+ * ffprobe. Only WebM is checked; MP4 is intentionally opaque and MOV/PNG-seq
+ * carry alpha through non-libvpx paths.
+ */
+export function webmAlphaAdvisory(format: string, probe: WebmAlphaProbe): string | undefined {
+  if (format !== "webm") return undefined;
+  if (!probe.probed || probe.alphaMode) return undefined;
+  return (
+    "The WebM output has no VP9 alpha sidecar (the ALPHA_MODE stream tag is absent), " +
+    "so transparency was flattened to opaque. Your ffmpeg/libvpx-vp9 build cannot emit " +
+    "the alpha plane on this platform. For guaranteed transparency, re-render with " +
+    "--format mov (ProRes 4444)."
+  );
+}
+
+/**
+ * Best-effort ffprobe of a file's first video stream for the ALPHA_MODE tag.
+ * Returns `{ probed: false }` on any failure (no ffprobe, spawn error,
+ * unreadable file, no video stream) — this is a diagnostic, never a reason to
+ * fail a completed render. The tag key is matched case-insensitively (ffprobe
+ * surfaces it as `ALPHA_MODE`; some builds lower-case it).
+ */
+function probeWebmAlpha(filePath: string): WebmAlphaProbe {
+  try {
+    const ffprobePath = findFFprobe();
+    if (!ffprobePath) return { probed: false, alphaMode: false };
+    const raw = execFileSync(
+      ffprobePath,
+      [
+        "-v",
+        "error",
+        "-select_streams",
+        "v:0",
+        "-show_entries",
+        "stream=codec_name:stream_tags=alpha_mode",
+        "-of",
+        "json",
+        filePath,
+      ],
+      { encoding: "utf-8", timeout: 15_000 },
+    );
+    const parsed = JSON.parse(raw) as {
+      streams?: Array<{ codec_name?: string; tags?: Record<string, string> }>;
+    };
+    const stream = parsed.streams?.[0];
+    if (!stream || typeof stream.codec_name !== "string") {
+      return { probed: false, alphaMode: false };
+    }
+    const tags = stream.tags ?? {};
+    const alphaMode = Object.entries(tags).some(
+      ([k, v]) => k.toLowerCase() === "alpha_mode" && String(v) === "1",
+    );
+    return { probed: true, alphaMode };
+  } catch {
+    return { probed: false, alphaMode: false };
+  }
+}
+
+/**
+ * After a completed WebM render, verify the output actually carries the alpha
+ * sidecar. Some ffmpeg/libvpx-vp9 builds silently produce opaque output — the
+ * render succeeds and looks fine in a player, but transparency is gone, which
+ * the user only discovers after compositing. Surface it loudly here with the
+ * concrete `--format mov` remedy. Best-effort and non-blocking; a build that
+ * DOES preserve alpha (ALPHA_MODE=1) stays silent.
+ */
+export function warnIfWebmAlphaDropped(outputPath: string, format: string, quiet: boolean): void {
+  if (quiet || format !== "webm") return;
+  const advisory = webmAlphaAdvisory(format, probeWebmAlpha(outputPath));
+  if (!advisory) return;
+  console.warn(`\n${c.warn("⚠")}  ${c.bold("Transparency not preserved")}`);
+  console.warn(`   ${c.dim(advisory)}\n`);
+}