diff --git a/src/apm_cli/adapters/client/base.py b/src/apm_cli/adapters/client/base.py
index 35e51e00..3741bafb 100644
--- a/src/apm_cli/adapters/client/base.py
+++ b/src/apm_cli/adapters/client/base.py
@@ -1,7 +1,10 @@
 """Base adapter interface for MCP clients."""
 
+import re
 from abc import ABC, abstractmethod
 
+_INPUT_VAR_RE = re.compile(r"\$\{input:([^}]+)\}")
+
 
 class MCPClientAdapter(ABC):
     """Base adapter for MCP clients."""
@@ -84,3 +87,33 @@ def _infer_registry_name(package):
             return "nuget"
 
         return ""
+
+    @staticmethod
+    def _warn_input_variables(mapping, server_name, runtime_label):
+        """Emit a warning for each ``${input:...}`` reference found in *mapping*.
+
+        Runtimes that do not support VS Code-style input prompts (Copilot CLI,
+        Codex CLI, etc.) should call this so users know their placeholders
+        will not be resolved at runtime.
+
+        Args:
+            mapping (dict): Header or env dict to scan.
+            server_name (str): Server name for the warning message.
+            runtime_label (str): Human-readable runtime name (e.g. "Copilot CLI").
+        """
+        if not mapping:
+            return
+        seen: set = set()
+        for value in mapping.values():
+            if not isinstance(value, str):
+                continue
+            for match in _INPUT_VAR_RE.finditer(value):
+                var_id = match.group(1)
+                if var_id in seen:
+                    continue
+                seen.add(var_id)
+                print(
+                    f"[!]  Warning: ${{input:{var_id}}} in server "
+                    f"'{server_name}' will not be resolved \u2014 "
+                    f"{runtime_label} does not support input variable prompts"
+                )
diff --git a/src/apm_cli/adapters/client/codex.py b/src/apm_cli/adapters/client/codex.py
index fe7da478..eda11493 100644
--- a/src/apm_cli/adapters/client/codex.py
+++ b/src/apm_cli/adapters/client/codex.py
@@ -181,6 +181,7 @@ def _format_server_config(self, server_info, env_overrides=None, runtime_vars=No
             config["args"] = raw["args"]
             if raw.get("env"):
                 config["env"] = raw["env"]
+                self._warn_input_variables(raw["env"], server_info.get("name", ""), "Codex CLI")
             return config
         
         # Note: Remote servers (SSE type) are handled in configure_mcp_server and rejected early
diff --git a/src/apm_cli/adapters/client/copilot.py b/src/apm_cli/adapters/client/copilot.py
index 77dfcae9..64147f39 100644
--- a/src/apm_cli/adapters/client/copilot.py
+++ b/src/apm_cli/adapters/client/copilot.py
@@ -173,6 +173,7 @@ def _format_server_config(self, server_info, env_overrides=None, runtime_vars=No
             config["args"] = raw["args"]
             if raw.get("env"):
                 config["env"] = raw["env"]
+                self._warn_input_variables(raw["env"], server_info.get("name", ""), "Copilot CLI")
             # Apply tools override if present
             tools_override = server_info.get("_apm_tools_override")
             if tools_override:
@@ -218,6 +219,10 @@ def _format_server_config(self, server_info, env_overrides=None, runtime_vars=No
                         resolved_value = self._resolve_env_variable(header_name, header_value, env_overrides)
                         config["headers"][header_name] = resolved_value
 
+            # Warn about unresolvable ${input:...} references in headers
+            if config.get("headers"):
+                self._warn_input_variables(config["headers"], server_info.get("name", ""), "Copilot CLI")
+
             # Apply tools override from MCP dependency overlay if present
             tools_override = server_info.get("_apm_tools_override")
             if tools_override:
diff --git a/src/apm_cli/adapters/client/vscode.py b/src/apm_cli/adapters/client/vscode.py
index 91372cf1..6932f86d 100644
--- a/src/apm_cli/adapters/client/vscode.py
+++ b/src/apm_cli/adapters/client/vscode.py
@@ -8,7 +8,7 @@
 import json
 import os
 from pathlib import Path
-from .base import MCPClientAdapter
+from .base import MCPClientAdapter, _INPUT_VAR_RE
 from ...registry.client import SimpleRegistryClient
 from ...registry.integration import RegistryIntegration
 
@@ -197,6 +197,9 @@ def _format_server_config(self, server_info):
             }
             if raw.get("env"):
                 server_config["env"] = raw["env"]
+                input_vars.extend(
+                    self._extract_input_variables(raw["env"], server_info.get("name", ""))
+                )
             return server_config, input_vars
         
         # Check for packages information
@@ -308,6 +311,9 @@ def _format_server_config(self, server_info):
                         "url": remote.get("url", ""),
                         "headers": headers,
                     }
+                    input_vars.extend(
+                        self._extract_input_variables(headers, server_info.get("name", ""))
+                    )
             # If no packages AND no endpoints/remotes, fail with clear error
             else:
                 packages = server_info.get("packages", [])
@@ -323,6 +329,36 @@ def _format_server_config(self, server_info):
         
         return server_config, input_vars
 
+    def _extract_input_variables(self, mapping, server_name):
+        """Scan dict values for ${input:...} references and return input variable definitions.
+
+        Args:
+            mapping (dict): Header or env dict whose values may contain
+                ``${input:<id>}`` placeholders.
+            server_name (str): Server name used in the description field.
+
+        Returns:
+            list[dict]: Input variable definitions (``promptString``, ``password: true``).
+                Duplicates within *mapping* are already deduplicated.
+        """
+        seen: set = set()
+        result: list = []
+        for value in (mapping or {}).values():
+            if not isinstance(value, str):
+                continue
+            for match in _INPUT_VAR_RE.finditer(value):
+                var_id = match.group(1)
+                if var_id in seen:
+                    continue
+                seen.add(var_id)
+                result.append({
+                    "type": "promptString",
+                    "id": var_id,
+                    "description": f"{var_id} for MCP server {server_name}",
+                    "password": True,
+                })
+        return result
+
     @staticmethod
     def _extract_package_args(package):
         """Extract positional arguments from a package entry.
diff --git a/tests/unit/test_vscode_adapter.py b/tests/unit/test_vscode_adapter.py
index 5cb277fe..3acbde02 100644
--- a/tests/unit/test_vscode_adapter.py
+++ b/tests/unit/test_vscode_adapter.py
@@ -8,6 +8,7 @@
 import pytest
 from unittest.mock import patch, MagicMock
 from apm_cli.adapters.client.vscode import VSCodeClientAdapter
+from apm_cli.adapters.client.base import MCPClientAdapter
 
 
 class TestVSCodeClientAdapter(unittest.TestCase):
@@ -724,5 +725,209 @@ def test_pypi_inferred_from_name_pattern(self, mock_get_path):
         self.assertEqual(server["args"], ["my-mcp-server"])
 
 
+class TestExtractInputVariables(unittest.TestCase):
+    """Tests for ${input:...} variable extraction in self-defined MCP servers."""
+
+    def setUp(self):
+        self.temp_dir = tempfile.TemporaryDirectory()
+        self.vscode_dir = os.path.join(self.temp_dir.name, ".vscode")
+        os.makedirs(self.vscode_dir, exist_ok=True)
+        self.temp_path = os.path.join(self.vscode_dir, "mcp.json")
+        with open(self.temp_path, "w") as f:
+            json.dump({"servers": {}, "inputs": []}, f)
+
+        self.mock_registry_patcher = patch('apm_cli.adapters.client.vscode.SimpleRegistryClient')
+        self.mock_registry_class = self.mock_registry_patcher.start()
+        self.mock_registry = MagicMock()
+        self.mock_registry_class.return_value = self.mock_registry
+
+        self.mock_integration_patcher = patch('apm_cli.adapters.client.vscode.RegistryIntegration')
+        self.mock_integration_class = self.mock_integration_patcher.start()
+        self.mock_integration = MagicMock()
+        self.mock_integration_class.return_value = self.mock_integration
+
+    def tearDown(self):
+        self.mock_registry_patcher.stop()
+        self.mock_integration_patcher.stop()
+        self.temp_dir.cleanup()
+
+    def test_extract_single_input_variable(self):
+        adapter = VSCodeClientAdapter()
+        result = adapter._extract_input_variables(
+            {"Authorization": "Bearer ${input:my-token}"}, "my-server"
+        )
+        assert len(result) == 1
+        assert result[0]["id"] == "my-token"
+        assert result[0]["type"] == "promptString"
+        assert result[0]["password"] is True
+        assert "my-server" in result[0]["description"]
+
+    def test_extract_multiple_input_variables(self):
+        adapter = VSCodeClientAdapter()
+        result = adapter._extract_input_variables(
+            {
+                "Authorization": "Bearer ${input:my-token}",
+                "X-Project": "${input:my-project}",
+            },
+            "my-server",
+        )
+        ids = {v["id"] for v in result}
+        assert ids == {"my-token", "my-project"}
+
+    def test_dedup_same_variable(self):
+        adapter = VSCodeClientAdapter()
+        result = adapter._extract_input_variables(
+            {
+                "Authorization": "Bearer ${input:shared-token}",
+                "X-Alt-Auth": "Token ${input:shared-token}",
+            },
+            "my-server",
+        )
+        assert len(result) == 1
+        assert result[0]["id"] == "shared-token"
+
+    def test_no_input_variables(self):
+        adapter = VSCodeClientAdapter()
+        result = adapter._extract_input_variables(
+            {"Content-Type": "application/json"}, "my-server"
+        )
+        assert result == []
+
+    def test_empty_mapping(self):
+        adapter = VSCodeClientAdapter()
+        assert adapter._extract_input_variables({}, "s") == []
+        assert adapter._extract_input_variables(None, "s") == []
+
+    @patch("apm_cli.adapters.client.vscode.VSCodeClientAdapter.get_config_path")
+    def test_self_defined_http_headers_generate_inputs(self, mock_get_path):
+        """End-to-end: self-defined HTTP server with ${input:} in headers."""
+        mock_get_path.return_value = self.temp_path
+
+        server_info = {
+            "name": "my-server",
+            "remotes": [
+                {
+                    "transport_type": "http",
+                    "url": "https://my-server.example.com/mcp/",
+                    "headers": [
+                        {"name": "Authorization", "value": "Bearer ${input:my-server-token}"},
+                        {"name": "X-Project", "value": "${input:my-server-project}"},
+                    ],
+                }
+            ],
+        }
+        self.mock_registry.find_server_by_reference.return_value = server_info
+
+        adapter = VSCodeClientAdapter()
+        result = adapter.configure_mcp_server(
+            server_url="my-server", server_name="my-server"
+        )
+
+        assert result is True
+        with open(self.temp_path, "r") as f:
+            config = json.load(f)
+
+        inputs = config["inputs"]
+        input_ids = {v["id"] for v in inputs}
+        assert "my-server-token" in input_ids
+        assert "my-server-project" in input_ids
+        for inp in inputs:
+            assert inp["type"] == "promptString"
+            assert inp["password"] is True
+
+    @patch("apm_cli.adapters.client.vscode.VSCodeClientAdapter.get_config_path")
+    def test_self_defined_stdio_env_generates_inputs(self, mock_get_path):
+        """End-to-end: self-defined stdio server with ${input:} in env."""
+        mock_get_path.return_value = self.temp_path
+
+        server_info = {
+            "name": "my-cli",
+            "_raw_stdio": {
+                "command": "my-cli",
+                "args": ["serve"],
+                "env": {"API_KEY": "${input:my-cli-api-key}"},
+            },
+        }
+        self.mock_registry.find_server_by_reference.return_value = server_info
+
+        adapter = VSCodeClientAdapter()
+        result = adapter.configure_mcp_server(
+            server_url="my-cli", server_name="my-cli"
+        )
+
+        assert result is True
+        with open(self.temp_path, "r") as f:
+            config = json.load(f)
+
+        inputs = config["inputs"]
+        assert len(inputs) == 1
+        assert inputs[0]["id"] == "my-cli-api-key"
+
+    @patch("apm_cli.adapters.client.vscode.VSCodeClientAdapter.get_config_path")
+    def test_input_variables_dedup_across_servers(self, mock_get_path):
+        """Input variables already present in config are not duplicated."""
+        mock_get_path.return_value = self.temp_path
+
+        # Pre-populate with an existing input
+        with open(self.temp_path, "w") as f:
+            json.dump(
+                {
+                    "servers": {},
+                    "inputs": [
+                        {"type": "promptString", "id": "my-server-token", "description": "existing", "password": True}
+                    ],
+                },
+                f,
+            )
+
+        server_info = {
+            "name": "my-server",
+            "remotes": [
+                {
+                    "transport_type": "http",
+                    "url": "https://example.com/mcp/",
+                    "headers": [
+                        {"name": "Authorization", "value": "Bearer ${input:my-server-token}"},
+                    ],
+                }
+            ],
+        }
+        self.mock_registry.find_server_by_reference.return_value = server_info
+
+        adapter = VSCodeClientAdapter()
+        adapter.configure_mcp_server(server_url="my-server", server_name="my-server")
+
+        with open(self.temp_path, "r") as f:
+            config = json.load(f)
+
+        token_entries = [i for i in config["inputs"] if i["id"] == "my-server-token"]
+        assert len(token_entries) == 1
+
+
+class TestWarnInputVariables(unittest.TestCase):
+    """Tests for _warn_input_variables on adapters that don't support input prompts."""
+
+    def test_warning_emitted_for_input_reference(self, ):
+        mapping = {"Authorization": "Bearer ${input:my-token}"}
+        with patch("builtins.print") as mock_print:
+            MCPClientAdapter._warn_input_variables(mapping, "my-server", "Copilot CLI")
+        mock_print.assert_called_once()
+        msg = mock_print.call_args[0][0]
+        assert "my-token" in msg
+        assert "Copilot CLI" in msg
+
+    def test_no_warning_for_plain_values(self):
+        mapping = {"Content-Type": "application/json"}
+        with patch("builtins.print") as mock_print:
+            MCPClientAdapter._warn_input_variables(mapping, "s", "Codex CLI")
+        mock_print.assert_not_called()
+
+    def test_no_warning_for_empty_mapping(self):
+        with patch("builtins.print") as mock_print:
+            MCPClientAdapter._warn_input_variables({}, "s", "Codex CLI")
+            MCPClientAdapter._warn_input_variables(None, "s", "Codex CLI")
+        mock_print.assert_not_called()
+
+
 if __name__ == "__main__":
     unittest.main()