diff --git a/src/utils/logger.ts b/src/utils/logger.ts
index 6ae5530..1d106b1 100644
--- a/src/utils/logger.ts
+++ b/src/utils/logger.ts
@@ -25,5 +25,7 @@ export function info(message: string): void {
 
 export function warn(message: string): void {
   if (quiet) return;
-  console.log(chalk.yellow(message));
+  // Warnings go to stderr so they never corrupt machine-readable stdout
+  // (e.g. `--json` output or a piped value); stdout is reserved for results.
+  console.error(chalk.yellow(message));
 }
diff --git a/tests/platform/resolve.test.ts b/tests/platform/resolve.test.ts
index f82b190..893c77b 100644
--- a/tests/platform/resolve.test.ts
+++ b/tests/platform/resolve.test.ts
@@ -93,7 +93,7 @@ describe("resolveProjectPlatform", () => {
       })
     );
 
-    const logSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const logSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
     const { resolveProjectPlatform } = await import("../../src/platform/resolve.js");
     const platform = await resolveProjectPlatform(testDir);
@@ -113,7 +113,7 @@ describe("resolveProjectPlatform", () => {
       })
     );
 
-    const logSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const logSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
     const { resolveProjectPlatform } = await import("../../src/platform/resolve.js");
     const platform = await resolveProjectPlatform(testDir);
@@ -128,7 +128,7 @@ describe("resolveProjectPlatform", () => {
     await mkdir(join(testDir, "bmalph"), { recursive: true });
     await writeFile(join(testDir, "bmalph/config.json"), "not valid json{{{");
 
-    const logSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const logSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
     const { resolveProjectPlatform } = await import("../../src/platform/resolve.js");
     const platform = await resolveProjectPlatform(testDir);
diff --git a/tests/utils/config.test.ts b/tests/utils/config.test.ts
index 04d82b3..ecd369a 100644
--- a/tests/utils/config.test.ts
+++ b/tests/utils/config.test.ts
@@ -58,7 +58,7 @@ describe("config", () => {
   it("returns null and warns when config file has invalid structure", async () => {
     await writeFile(join(testDir, "bmalph/config.json"), JSON.stringify({ garbage: true }));
 
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
     const result = await readConfig(testDir);
 
@@ -123,7 +123,7 @@ platform: claude-code
 
   it("returns null and warns for malformed YAML", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "planning_artifacts: [invalid");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining("Error reading BMAD config"));
@@ -132,7 +132,7 @@ platform: claude-code
 
   it("returns null and warns for non-string planning_artifacts field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "planning_artifacts: 123\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
@@ -143,7 +143,7 @@ platform: claude-code
 
   it("returns null and warns for boolean planning_artifacts field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "planning_artifacts: true\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
@@ -154,7 +154,7 @@ platform: claude-code
 
   it("returns null and warns for object planning_artifacts field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "planning_artifacts:\n  foo: bar\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
@@ -165,7 +165,7 @@ platform: claude-code
 
   it("returns null and warns for empty YAML file", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining("Error reading BMAD config"));
@@ -174,7 +174,7 @@ platform: claude-code
 
   it("returns null and warns when YAML parses to a scalar", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "just a string\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining("Error reading BMAD config"));
@@ -183,7 +183,7 @@ platform: claude-code
 
   it("returns null and warns when YAML parses to an array", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "- item1\n- item2\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining("Error reading BMAD config"));
@@ -192,7 +192,7 @@ platform: claude-code
 
   it("returns null and warns for non-string platform field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "platform: 123\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
@@ -203,7 +203,7 @@ platform: claude-code
 
   it("returns null and warns for non-string project_name field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "project_name: true\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
@@ -214,7 +214,7 @@ platform: claude-code
 
   it("returns null and warns for non-string output_folder field", async () => {
     await writeFile(join(testDir, "_bmad/config.yaml"), "output_folder: 42\n");
-    const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
     const result = await readBmadConfig(testDir);
     expect(result).toBeNull();
     expect(warnSpy).toHaveBeenCalledWith(
diff --git a/tests/utils/logger.test.ts b/tests/utils/logger.test.ts
index bbd28dc..a5cad57 100644
--- a/tests/utils/logger.test.ts
+++ b/tests/utils/logger.test.ts
@@ -12,14 +12,17 @@ vi.mock("chalk", () => ({
 
 describe("logger", () => {
   let consoleSpy: ReturnType<typeof vi.spyOn>;
+  let consoleErrorSpy: ReturnType<typeof vi.spyOn>;
 
   beforeEach(() => {
     vi.resetModules();
     consoleSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    consoleErrorSpy = vi.spyOn(console, "error").mockImplementation(() => {});
   });
 
   afterEach(() => {
     consoleSpy.mockRestore();
+    consoleErrorSpy.mockRestore();
     vi.restoreAllMocks();
   });
 
@@ -100,6 +103,7 @@ describe("logger", () => {
       warn("warning should not appear");
 
       expect(consoleSpy).not.toHaveBeenCalled();
+      expect(consoleErrorSpy).not.toHaveBeenCalled();
     });
 
     it("resumes normal output when quiet is disabled", async () => {
@@ -127,13 +131,21 @@ describe("logger", () => {
   });
 
   describe("warn", () => {
-    it("outputs message with yellow color", async () => {
+    it("outputs message with yellow color to stderr", async () => {
       const { warn } = await import("../../src/utils/logger.js");
 
       warn("warning message");
 
-      expect(consoleSpy).toHaveBeenCalledWith(expect.stringContaining("[yellow]"));
-      expect(consoleSpy).toHaveBeenCalledWith(expect.stringContaining("warning message"));
+      expect(consoleErrorSpy).toHaveBeenCalledWith(expect.stringContaining("[yellow]"));
+      expect(consoleErrorSpy).toHaveBeenCalledWith(expect.stringContaining("warning message"));
+    });
+
+    it("does not write warnings to stdout", async () => {
+      const { warn } = await import("../../src/utils/logger.js");
+
+      warn("warning message");
+
+      expect(consoleSpy).not.toHaveBeenCalled();
     });
   });
 });
diff --git a/tests/utils/state.test.ts b/tests/utils/state.test.ts
index d0b81ef..e4cfb6d 100644
--- a/tests/utils/state.test.ts
+++ b/tests/utils/state.test.ts
@@ -58,7 +58,7 @@ describe("state", () => {
         JSON.stringify({ garbage: true })
       );
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readState(testDir);
 
@@ -230,7 +230,7 @@ describe("state", () => {
       await mkdir(join(testDir, ".ralph"), { recursive: true });
       await writeFile(join(testDir, ".ralph/status.json"), '"just a string"');
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);
 
@@ -250,7 +250,7 @@ describe("state", () => {
       await mkdir(join(testDir, ".ralph"), { recursive: true });
       await writeFile(join(testDir, ".ralph/status.json"), '{"loopCount": "not-a-number"}');
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);
 
@@ -278,7 +278,7 @@ describe("state", () => {
         })
       );
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);
 
@@ -305,7 +305,7 @@ describe("state", () => {
         })
       );
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);
 
@@ -332,7 +332,7 @@ describe("state", () => {
         })
       );
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);
 
@@ -435,7 +435,7 @@ describe("state", () => {
         })
       );
 
-      const warnSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+      const warnSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 
       const result = await readRalphStatus(testDir);