diff --git a/src/cli/plugins-cli.list.test.ts b/src/cli/plugins-cli.list.test.ts
index ed45cb96a08..5abd73f54ba 100644
--- a/src/cli/plugins-cli.list.test.ts
+++ b/src/cli/plugins-cli.list.test.ts
@@ -78,6 +78,40 @@ describe("plugins cli list", () => {
     expect(runtimeLogs).toContain("No plugin issues detected.");
   });
 
+  it("reports config-selected plugin source shadowing in doctor output", async () => {
+    buildPluginDiagnosticsReport.mockReturnValue({
+      plugins: [
+        createPluginRecord({
+          id: "discord",
+          origin: "config",
+          source: "/tmp/openclaw-upstream/extensions/discord/index.ts",
+          status: "error",
+          error: "Cannot find module 'chalk'",
+        }),
+      ],
+      diagnostics: [
+        {
+          level: "warn",
+          pluginId: "discord",
+          source: "/tmp/openclaw/npm/node_modules/@openclaw/discord/index.ts",
+          message:
+            "duplicate plugin id resolved by explicit config-selected plugin; global plugin will be overridden by config plugin (/tmp/openclaw-upstream/extensions/discord/index.ts)",
+        },
+      ],
+    });
+
+    await runPluginsCommand(["plugins", "doctor"]);
+
+    const output = runtimeLogs.join("\n");
+    expect(output).toContain("Plugin source shadowing:");
+    expect(output).toContain(
+      "discord: duplicate plugin id resolved by explicit config-selected plugin",
+    );
+    expect(output).toContain("active: /tmp/openclaw-upstream/extensions/discord/index.ts");
+    expect(output).toContain("shadowed: /tmp/openclaw/npm/node_modules/@openclaw/discord/index.ts");
+    expect(output).toContain("openclaw plugins registry --refresh");
+  });
+
   it("reports persisted plugin registry state without refreshing", async () => {
     inspectPluginRegistry.mockResolvedValue({
       state: "stale",
diff --git a/src/cli/plugins-cli.ts b/src/cli/plugins-cli.ts
index 631271189e5..10eded74098 100644
--- a/src/cli/plugins-cli.ts
+++ b/src/cli/plugins-cli.ts
@@ -5,6 +5,7 @@ import { tracePluginLifecyclePhaseAsync } from "../plugins/plugin-lifecycle-trac
 import { defaultRuntime } from "../runtime.js";
 import { formatDocsLink } from "../terminal/links.js";
 import { theme } from "../terminal/theme.js";
+import { shortenHomeInString } from "../utils.js";
 import type { PluginInspectOptions } from "./plugins-inspect-command.js";
 import type { PluginsListOptions } from "./plugins-list-command.js";
 import { applyParentDefaultHelpAction } from "./program/parent-default-help.js";
@@ -62,6 +63,14 @@ function matchesPluginId(plugin: { id: string }, id: string) {
   return plugin.id === id;
 }
 
+function isConfigSelectedShadowDiagnostic(entry: { level?: string; message?: string }): boolean {
+  return (
+    entry.level === "warn" &&
+    typeof entry.message === "string" &&
+    entry.message.includes("duplicate plugin id resolved by explicit config-selected plugin")
+  );
+}
+
 export function registerPluginsCli(program: Command) {
   const plugins = program
     .command("plugins")
@@ -336,9 +345,15 @@ export function registerPluginsCli(program: Command) {
       const report = buildPluginDiagnosticsReport({ effectiveOnly: true });
       const errors = report.plugins.filter((p) => p.status === "error");
       const diags = report.diagnostics.filter((d) => d.level === "error");
+      const shadowed = report.diagnostics.filter(isConfigSelectedShadowDiagnostic);
       const compatibility = buildPluginCompatibilityNotices({ report });
 
-      if (errors.length === 0 && diags.length === 0 && compatibility.length === 0) {
+      if (
+        errors.length === 0 &&
+        diags.length === 0 &&
+        shadowed.length === 0 &&
+        compatibility.length === 0
+      ) {
         defaultRuntime.log("No plugin issues detected.");
         return;
       }
@@ -361,6 +376,31 @@ export function registerPluginsCli(program: Command) {
           lines.push(`- ${target}${diag.message}`);
         }
       }
+      if (shadowed.length > 0) {
+        if (lines.length > 0) {
+          lines.push("");
+        }
+        lines.push(theme.warn("Plugin source shadowing:"));
+        for (const diag of shadowed) {
+          const active = report.plugins.find((plugin) => plugin.id === diag.pluginId);
+          const target = diag.pluginId ? `${diag.pluginId}: ` : "";
+          lines.push(`- ${target}${diag.message}`);
+          if (active) {
+            lines.push(`  active: ${shortenHomeInString(active.source)} (${active.origin})`);
+            if (active.status === "error") {
+              lines.push(`  active status: error${active.error ? `: ${active.error}` : ""}`);
+            }
+          }
+          if (diag.source) {
+            lines.push(`  shadowed: ${shortenHomeInString(diag.source)}`);
+          }
+          lines.push("  repair:");
+          lines.push("    openclaw plugins inspect " + (diag.pluginId ?? "<plugin-id>"));
+          lines.push("    edit or remove the config-selected plugin source");
+          lines.push("    openclaw plugins registry --refresh");
+          lines.push("    openclaw gateway restart --force");
+        }
+      }
       if (compatibility.length > 0) {
         if (lines.length > 0) {
           lines.push("");
diff --git a/src/cli/plugins-install-persist.test.ts b/src/cli/plugins-install-persist.test.ts
index 9d01a58863f..4ff4334e3ed 100644
--- a/src/cli/plugins-install-persist.test.ts
+++ b/src/cli/plugins-install-persist.test.ts
@@ -3,6 +3,7 @@ import type { OpenClawConfig } from "../config/config.js";
 import {
   applyExclusiveSlotSelection,
   buildPluginDiagnosticsReport,
+  buildPluginSnapshotReport,
   clearPluginRegistryLoadCache,
   enablePluginInConfig,
   loadPluginManifestRegistry,
@@ -124,6 +125,64 @@ describe("persistPluginInstall", () => {
     ).toBe(true);
   });
 
+  it("warns when an installed npm plugin remains shadowed by a config-selected source", async () => {
+    const { persistPluginInstall } = await import("./plugins-install-persist.js");
+    const baseConfig = {
+      plugins: {
+        entries: {},
+      },
+    } as OpenClawConfig;
+    const enabledConfig = {
+      plugins: {
+        entries: {
+          discord: { enabled: true },
+        },
+      },
+    } as OpenClawConfig;
+    enablePluginInConfig.mockReturnValue({ config: enabledConfig });
+    buildPluginSnapshotReport.mockReturnValue({
+      plugins: [
+        {
+          id: "discord",
+          origin: "config",
+          source: "/tmp/openclaw-upstream/extensions/discord/index.ts",
+          status: "error",
+        },
+      ],
+      diagnostics: [],
+    });
+
+    const next = await persistPluginInstall({
+      snapshot: {
+        config: baseConfig,
+        baseHash: "config-1",
+      },
+      pluginId: "discord",
+      install: {
+        source: "npm",
+        spec: "@openclaw/discord",
+        installPath: "/tmp/openclaw/npm/node_modules/@openclaw/discord/index.ts",
+      },
+    });
+
+    expect(next).toEqual(enabledConfig);
+    expect(buildPluginSnapshotReport).toHaveBeenCalledWith({
+      config: enabledConfig,
+      effectiveOnly: true,
+      onlyPluginIds: ["discord"],
+    });
+    expect(runtimeLogs.join("\n")).toContain(
+      'Warning: installed plugin "discord" is not the active source',
+    );
+    expect(runtimeLogs.join("\n")).toContain(
+      "active config source: /tmp/openclaw-upstream/extensions/discord/index.ts",
+    );
+    expect(runtimeLogs.join("\n")).toContain(
+      "installed npm source: /tmp/openclaw/npm/node_modules/@openclaw/discord/index.ts",
+    );
+    expect(runtimeLogs.join("\n")).toContain("openclaw plugins doctor");
+  });
+
   it("invalidates runtime cache even when registry refresh fails", async () => {
     const { persistPluginInstall } = await import("./plugins-install-persist.js");
     const baseConfig = {
diff --git a/src/cli/plugins-install-persist.ts b/src/cli/plugins-install-persist.ts
index a9d2775a750..b032388ee5d 100644
--- a/src/cli/plugins-install-persist.ts
+++ b/src/cli/plugins-install-persist.ts
@@ -9,8 +9,10 @@ import {
 } from "../plugins/installed-plugin-index-records.js";
 import type { PluginInstallUpdate } from "../plugins/installs.js";
 import { tracePluginLifecyclePhaseAsync } from "../plugins/plugin-lifecycle-trace.js";
+import { buildPluginSnapshotReport } from "../plugins/status.js";
 import { defaultRuntime, type RuntimeEnv } from "../runtime.js";
 import { theme } from "../terminal/theme.js";
+import { shortenHomePath } from "../utils.js";
 import {
   applySlotSelectionForPlugin,
   enableInternalHookEntries,
@@ -58,6 +60,41 @@ export type ConfigSnapshotForInstallPersist = {
   baseHash: string | undefined;
 };
 
+function logShadowedNpmInstallWarning(params: {
+  config: OpenClawConfig;
+  pluginId: string;
+  install: Omit<PluginInstallUpdate, "pluginId">;
+  runtime: RuntimeEnv;
+}): void {
+  if (params.install.source !== "npm") {
+    return;
+  }
+  const installedSource = params.install.installPath ?? params.install.sourcePath;
+  if (!installedSource) {
+    return;
+  }
+  const report = buildPluginSnapshotReport({
+    config: params.config,
+    effectiveOnly: true,
+    onlyPluginIds: [params.pluginId],
+  });
+  const active = report.plugins.find((plugin) => plugin.id === params.pluginId);
+  if (!active || active.origin !== "config" || active.source === installedSource) {
+    return;
+  }
+
+  params.runtime.log(
+    theme.warn(
+      [
+        `Warning: installed plugin "${params.pluginId}" is not the active source because a config-selected plugin with the same id is currently selected:`,
+        `  active config source: ${shortenHomePath(active.source)}`,
+        `  installed npm source: ${shortenHomePath(installedSource)}`,
+        "Run `openclaw plugins doctor` for repair options.",
+      ].join("\n"),
+    ),
+  );
+}
+
 export async function persistPluginInstall(params: {
   snapshot: ConfigSnapshotForInstallPersist;
   pluginId: string;
@@ -127,6 +164,12 @@ export async function persistPluginInstall(params: {
     runtime.log(theme.warn(params.warningMessage));
   }
   runtime.log(params.successMessage ?? `Installed plugin: ${params.pluginId}`);
+  logShadowedNpmInstallWarning({
+    config: next,
+    pluginId: params.pluginId,
+    install: params.install,
+    runtime,
+  });
   runtime.log("Restart the gateway to load plugins.");
   return next;
 }