diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index c33281e2b..eb4c306bf 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -33,6 +33,7 @@
 import json
 import json5
 import stat
+import shlex
 import yaml
 from pathlib import Path
 from typing import Any, Optional
@@ -92,6 +93,36 @@ def _build_ai_assistant_help() -> str:
     return base_help + " Use " + aliases_text + "."
 AI_ASSISTANT_HELP = _build_ai_assistant_help()
 
+
+def _build_integration_equivalent(
+    integration_key: str,
+    ai_commands_dir: str | None = None,
+) -> str:
+    """Build the modern --integration equivalent for legacy --ai usage."""
+
+    parts = [f"--integration {integration_key}"]
+    if integration_key == "generic" and ai_commands_dir:
+        parts.append(
+            f'--integration-options="--commands-dir {shlex.quote(ai_commands_dir)}"'
+        )
+    return " ".join(parts)
+
+
+def _build_ai_deprecation_warning(
+    integration_key: str,
+    ai_commands_dir: str | None = None,
+) -> str:
+    """Build the legacy --ai deprecation warning message."""
+
+    replacement = _build_integration_equivalent(
+        integration_key,
+        ai_commands_dir=ai_commands_dir,
+    )
+    return (
+        "[bold]--ai[/bold] is deprecated and will no longer be available in version 1.0.0 or later.\n\n"
+        f"Use [bold]{replacement}[/bold] instead."
+    )
+
 SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
 
 CLAUDE_LOCAL_PATH = Path.home() / ".claude" / "local" / "claude"
@@ -957,6 +988,7 @@ def init(
     """
 
     show_banner()
+    ai_deprecation_warning: str | None = None
 
     # Detect when option values are likely misinterpreted flags (parameter ordering issue)
     if ai_assistant and ai_assistant.startswith("--"):
@@ -995,6 +1027,10 @@ def init(
         if not resolved_integration:
             console.print(f"[red]Error:[/red] Unknown agent '{ai_assistant}'. Choose from: {', '.join(sorted(INTEGRATION_REGISTRY))}")
             raise typer.Exit(1)
+        ai_deprecation_warning = _build_ai_deprecation_warning(
+            resolved_integration.key,
+            ai_commands_dir=ai_commands_dir,
+        )
 
     # Deprecation warnings for --ai-skills and --ai-commands-dir (only when
     # an integration has been resolved from --ai or --integration)
@@ -1428,6 +1464,16 @@ def init(
             console.print()
             console.print(security_notice)
 
+    if ai_deprecation_warning:
+        deprecation_notice = Panel(
+            ai_deprecation_warning,
+            title="[bold red]Deprecation Warning[/bold red]",
+            border_style="red",
+            padding=(1, 2),
+        )
+        console.print()
+        console.print(deprecation_notice)
+
     steps_lines = []
     if not here:
         steps_lines.append(f"1. Go to the project folder: [cyan]cd {project_name}[/cyan]")
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index 1e23e35a7..bd73ccd66 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -5,6 +5,14 @@
 
 import yaml
 
+from tests.conftest import strip_ansi
+
+
+def _normalize_cli_output(output: str) -> str:
+    output = strip_ansi(output)
+    output = " ".join(output.split())
+    return output.strip()
+
 
 class TestInitIntegrationFlag:
     def test_integration_and_ai_mutually_exclusive(self, tmp_path):
@@ -77,6 +85,59 @@ def test_ai_copilot_auto_promotes(self, tmp_path):
         assert result.exit_code == 0
         assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
 
+    def test_ai_emits_deprecation_warning_with_integration_replacement(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "warn-ai"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "copilot", "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        normalized_output = _normalize_cli_output(result.output)
+        assert result.exit_code == 0, result.output
+        assert "Deprecation Warning" in normalized_output
+        assert "--ai" in normalized_output
+        assert "deprecated" in normalized_output
+        assert "no longer be available" in normalized_output
+        assert "1.0.0" in normalized_output
+        assert "--integration copilot" in normalized_output
+        assert normalized_output.index("Deprecation Warning") < normalized_output.index("Next Steps")
+        assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
+
+    def test_ai_generic_warning_suggests_integration_options_equivalent(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "warn-generic"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "generic", "--ai-commands-dir", ".myagent/commands",
+                "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        normalized_output = _normalize_cli_output(result.output)
+        assert result.exit_code == 0, result.output
+        assert "Deprecation Warning" in normalized_output
+        assert "--integration generic" in normalized_output
+        assert "--integration-options" in normalized_output
+        assert ".myagent/commands" in normalized_output
+        assert normalized_output.index("Deprecation Warning") < normalized_output.index("Next Steps")
+        assert (project / ".myagent" / "commands" / "speckit.plan.md").exists()
+
     def test_ai_claude_here_preserves_preexisting_commands(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app