diff --git a/src/features/subagents/copilot-subagent.test.ts b/src/features/subagents/copilot-subagent.test.ts
index ae4608f52..cd8503f79 100644
--- a/src/features/subagents/copilot-subagent.test.ts
+++ b/src/features/subagents/copilot-subagent.test.ts
@@ -96,6 +96,81 @@ Plan tasks`;
 
       expect(subagent.getFrontmatter().tools).toEqual(["agent/runSubagent"]);
     });
+
+    it("converts .md extension to .agent.md in output file path", () => {
+      const rulesyncSubagent = new RulesyncSubagent({
+        baseDir: testDir,
+        relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+        relativeFilePath: "planner.md",
+        frontmatter: {
+          targets: ["copilot"],
+          name: "planner",
+          description: "Plan things",
+          copilot: {},
+        },
+        body: "Plan tasks",
+        validate: true,
+      });
+
+      const subagent = CopilotSubagent.fromRulesyncSubagent({
+        baseDir: testDir,
+        relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+        rulesyncSubagent,
+        validate: true,
+      }) as CopilotSubagent;
+
+      expect(subagent.getRelativeFilePath()).toBe("planner.agent.md");
+    });
+
+    it("preserves .agent.md extension when already present", () => {
+      const rulesyncSubagent = new RulesyncSubagent({
+        baseDir: testDir,
+        relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+        relativeFilePath: "planner.agent.md",
+        frontmatter: {
+          targets: ["copilot"],
+          name: "planner",
+          description: "Plan things",
+          copilot: {},
+        },
+        body: "Plan tasks",
+        validate: true,
+      });
+
+      const subagent = CopilotSubagent.fromRulesyncSubagent({
+        baseDir: testDir,
+        relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+        rulesyncSubagent,
+        validate: true,
+      }) as CopilotSubagent;
+
+      expect(subagent.getRelativeFilePath()).toBe("planner.agent.md");
+    });
+
+    it("throws when source file path does not end in .md", () => {
+      const rulesyncSubagent = new RulesyncSubagent({
+        baseDir: testDir,
+        relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+        relativeFilePath: "planner.txt",
+        frontmatter: {
+          targets: ["copilot"],
+          name: "planner",
+          description: "Plan things",
+          copilot: {},
+        },
+        body: "Plan tasks",
+        validate: true,
+      });
+
+      expect(() =>
+        CopilotSubagent.fromRulesyncSubagent({
+          baseDir: testDir,
+          relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
+          rulesyncSubagent,
+          validate: true,
+        }),
+      ).toThrow("Expected .md file path");
+    });
   });
 
   describe("toRulesyncSubagent", () => {
@@ -124,6 +199,25 @@ Plan tasks`;
       });
       expect(rulesyncSubagent.getBody()).toBe("Plan tasks");
     });
+
+    it("converts .agent.md back to .md for rulesync file path", () => {
+      const subagent = new CopilotSubagent({
+        baseDir: testDir,
+        relativeDirPath: ".github/agents",
+        relativeFilePath: "planner.agent.md",
+        frontmatter: {
+          name: "planner",
+          description: "Plan things",
+        },
+        body: "Plan tasks",
+        fileContent: validContent,
+        validate: true,
+      });
+
+      const rulesyncSubagent = subagent.toRulesyncSubagent();
+
+      expect(rulesyncSubagent.getRelativeFilePath()).toBe("planner.md");
+    });
   });
 
   describe("fromFile", () => {
diff --git a/src/features/subagents/copilot-subagent.ts b/src/features/subagents/copilot-subagent.ts
index 5b4b62a28..4f9e03c8e 100644
--- a/src/features/subagents/copilot-subagent.ts
+++ b/src/features/subagents/copilot-subagent.ts
@@ -31,6 +31,25 @@ type CopilotSubagentParams = {
   body: string;
 } & AiFileParams;
 
+const AGENT_MD_EXTENSION = ".agent.md";
+
+const toAgentMdFilePath = (filePath: string): string => {
+  if (filePath.endsWith(AGENT_MD_EXTENSION)) {
+    return filePath;
+  }
+  if (filePath.endsWith(".md")) {
+    return filePath.slice(0, -3) + AGENT_MD_EXTENSION;
+  }
+  throw new Error(`Expected .md file path, got: ${filePath}`);
+};
+
+const fromAgentMdFilePath = (filePath: string): string => {
+  if (filePath.endsWith(AGENT_MD_EXTENSION)) {
+    return filePath.slice(0, -AGENT_MD_EXTENSION.length) + ".md";
+  }
+  return filePath;
+};
+
 const normalizeTools = (tools: string | string[] | undefined): string[] => {
   if (!tools) {
     return [];
@@ -98,7 +117,7 @@ export class CopilotSubagent extends ToolSubagent {
       frontmatter: rulesyncFrontmatter,
       body: this.body,
       relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
-      relativeFilePath: this.getRelativeFilePath(),
+      relativeFilePath: fromAgentMdFilePath(this.getRelativeFilePath()),
       validate: true,
     });
   }
@@ -134,7 +153,7 @@ export class CopilotSubagent extends ToolSubagent {
       frontmatter: copilotFrontmatter,
       body,
       relativeDirPath: paths.relativeDirPath,
-      relativeFilePath: rulesyncSubagent.getRelativeFilePath(),
+      relativeFilePath: toAgentMdFilePath(rulesyncSubagent.getRelativeFilePath()),
       fileContent,
       validate,
       global,
diff --git a/src/features/subagents/subagents-processor.test.ts b/src/features/subagents/subagents-processor.test.ts
index 7e4012eb2..67440afb7 100644
--- a/src/features/subagents/subagents-processor.test.ts
+++ b/src/features/subagents/subagents-processor.test.ts
@@ -646,7 +646,7 @@ description: Copilot agent description
 ---
 Copilot agent content`;
 
-      await writeFileContent(join(subagentsDir, "copilot-agent.md"), subagentContent);
+      await writeFileContent(join(subagentsDir, "copilot-agent.agent.md"), subagentContent);
 
       const toolFiles = await processor.loadToolFiles();
 
diff --git a/src/features/subagents/subagents-processor.ts b/src/features/subagents/subagents-processor.ts
index 9675b99d2..62f8a0a9a 100644
--- a/src/features/subagents/subagents-processor.ts
+++ b/src/features/subagents/subagents-processor.ts
@@ -119,7 +119,7 @@ const toolSubagentFactories = new Map<SubagentsProcessorToolTarget, ToolSubagent
     "copilot",
     {
       class: CopilotSubagent,
-      meta: { supportsSimulated: false, supportsGlobal: false, filePattern: "*.md" },
+      meta: { supportsSimulated: false, supportsGlobal: false, filePattern: "*.agent.md" },
     },
   ],
   [