diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
index 5cc34d2b1d..747b7e9cab 100644
--- a/src/specify_cli/integrations/copilot/__init__.py
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -57,6 +57,17 @@ def _allow_all() -> bool:
     return True
 
 
+def _warn_legacy_markdown_default() -> None:
+    """Warn that Copilot's default markdown scaffold is being phased out."""
+    warnings.warn(
+        "Copilot legacy markdown mode is deprecated and will stop being the "
+        'default in a future Spec Kit release; pass --integration-options "--skills" '
+        "to opt in to Copilot skills mode now.",
+        UserWarning,
+        stacklevel=3,
+    )
+
+
 class _CopilotSkillsHelper(SkillsIntegration):
     """Internal helper used when Copilot is scaffolded in skills mode.
 
@@ -316,6 +327,8 @@ def setup(
         self._skills_mode = bool(parsed_options.get("skills"))
         if self._skills_mode:
             return self._setup_skills(project_root, manifest, parsed_options, **opts)
+        if "skills" not in parsed_options:
+            _warn_legacy_markdown_default()
         return self._setup_default(project_root, manifest, parsed_options, **opts)
 
     def _setup_default(
diff --git a/tests/integrations/test_integration_copilot.py b/tests/integrations/test_integration_copilot.py
index 8a7c8ec995..41261ba1cb 100644
--- a/tests/integrations/test_integration_copilot.py
+++ b/tests/integrations/test_integration_copilot.py
@@ -2,7 +2,9 @@
 
 import json
 import os
+import warnings
 
+import pytest
 import yaml
 
 from specify_cli.integrations import get_integration
@@ -34,6 +36,31 @@ def test_setup_creates_agent_md_files(self, tmp_path):
             assert f.parent == tmp_path / ".github" / "agents"
             assert f.name.endswith(".agent.md")
 
+    def test_setup_warns_legacy_markdown_default_is_deprecated(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+
+        with pytest.warns(UserWarning, match="Copilot legacy markdown mode is deprecated"):
+            created = copilot.setup(tmp_path, m)
+
+        assert any(f.name.endswith(".agent.md") for f in created)
+
+    def test_skills_setup_does_not_warn_about_legacy_default(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+
+        with warnings.catch_warnings(record=True) as caught:
+            warnings.simplefilter("always")
+            created = copilot.setup(tmp_path, m, parsed_options={"skills": True})
+
+        assert not any(
+            "Copilot legacy markdown mode is deprecated" in str(item.message)
+            for item in caught
+        )
+        assert any(f.name == "SKILL.md" for f in created)
+
     def test_setup_creates_companion_prompts(self, tmp_path):
         from specify_cli.integrations.copilot import CopilotIntegration
         copilot = CopilotIntegration()
@@ -295,6 +322,51 @@ def test_complete_file_inventory_ps(self, tmp_path):
             f"Extra: {sorted(set(actual) - set(expected))}"
         )
 
+    def test_default_cli_init_warns_legacy_markdown_is_deprecated(self, tmp_path):
+        """Default Copilot init should warn users about the future skills default."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        project = tmp_path / "default-warning"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            with pytest.warns(
+                UserWarning,
+                match="Copilot legacy markdown mode is deprecated",
+            ):
+                result = CliRunner().invoke(app, [
+                    "init", "--here", "--integration", "copilot", "--script", "sh",
+                ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, result.output
+
+    def test_skills_cli_init_does_not_warn_about_legacy_markdown(self, tmp_path):
+        """Explicit Copilot skills mode should not warn about the legacy default."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        project = tmp_path / "skills-no-warning"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            with warnings.catch_warnings(record=True) as caught:
+                warnings.simplefilter("always")
+                result = CliRunner().invoke(app, [
+                    "init", "--here", "--integration", "copilot",
+                    "--integration-options", "--skills", "--script", "sh",
+                ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, result.output
+        assert not any(
+            "Copilot legacy markdown mode is deprecated" in str(item.message)
+            for item in caught
+        )
+
 
 class TestCopilotSkillsMode:
     """Tests for Copilot integration in --skills mode."""