diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index f6f08af8b..8ccb05eb1 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -3348,6 +3348,47 @@ async function runTests() {
       await fs.remove(tmp).catch(() => {});
     }
 
+    // ---- Multiple module definitions: deepest-first default + chooser ----
+    // Both src/ and src/skills/ carry module.yaml + module-help.csv. Headless
+    // resolution must take the deepest (src/skills); an interactive caller can
+    // override via chooseModuleDefinition, which receives enriched metadata.
+    {
+      const tmp = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-multimod-'));
+      const csv =
+        'module,skill,display-name,menu-code,description,action,args,phase,preceded-by,followed-by,required,output-location,outputs\n';
+      const srcDir = path.join(tmp, 'src');
+      const skillsDir = path.join(srcDir, 'skills');
+      await fs.ensureDir(skillsDir);
+      await fs.writeFile(path.join(srcDir, 'module.yaml'), 'code: outer\nname: Outer\ndescription: at src\n', 'utf8');
+      await fs.writeFile(path.join(srcDir, 'module-help.csv'), csv, 'utf8');
+      await fs.writeFile(path.join(skillsDir, 'module.yaml'), 'code: inner\nname: Inner\ndescription: at src/skills\n', 'utf8');
+      await fs.writeFile(path.join(skillsDir, 'module-help.csv'), csv, 'utf8');
+      for (const name of ['skill-a', 'skill-b']) {
+        const skill = path.join(skillsDir, name);
+        await fs.ensureDir(skill);
+        await fs.writeFile(path.join(skill, 'SKILL.md'), `---\nname: ${name}\ndescription: x\n---\n`, 'utf8');
+      }
+      const plugin = { name: 'multi', source: '.', skills: ['./src/skills/skill-a', './src/skills/skill-b'] };
+
+      const def = await new PluginResolver().resolve(tmp, plugin);
+      assert(def[0].code === 'inner', 'with no chooser, the deepest module definition (src/skills) is used by default');
+
+      let seen = null;
+      const picked = await new PluginResolver().resolve(tmp, plugin, {
+        chooseModuleDefinition: async (candidates) => {
+          seen = candidates;
+          return candidates.find((c) => c.code === 'outer');
+        },
+      });
+      assert(Array.isArray(seen) && seen.length === 2, 'chooser receives all candidates when more than one is found');
+      assert(
+        seen.every((c) => typeof c.relativePath === 'string' && 'name' in c && 'description' in c),
+        'chooser candidates are enriched with relativePath + module.yaml metadata',
+      );
+      assert(picked[0].code === 'outer', "chooser's selection (src) overrides the deepest default");
+      await fs.remove(tmp).catch(() => {});
+    }
+
     // ---- End-to-end install of a new-system module via OfficialModules ----
     {
       const tmp = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-pj-install-'));
diff --git a/tools/installer/modules/custom-module-manager.js b/tools/installer/modules/custom-module-manager.js
index 8a5ea8863..50dedb16e 100644
--- a/tools/installer/modules/custom-module-manager.js
+++ b/tools/installer/modules/custom-module-manager.js
@@ -572,12 +572,14 @@ class CustomModuleManager {
    * @param {Object} plugin - Raw plugin object from marketplace.json
    * @param {string} [sourceUrl] - Original URL for manifest tracking (null for local)
    * @param {string} [localPath] - Local source path for manifest tracking (null for URLs)
+   * @param {Object} [options] - Forwarded to PluginResolver.resolve (e.g.
+   *   chooseModuleDefinition for interactive disambiguation).
    * @returns {Promise<Array<Object>>} Array of ResolvedModule objects
    */
-  async resolvePlugin(repoPath, plugin, sourceUrl, localPath) {
+  async resolvePlugin(repoPath, plugin, sourceUrl, localPath, options = {}) {
     const { PluginResolver } = require('./plugin-resolver');
     const resolver = new PluginResolver();
-    const resolved = await resolver.resolve(repoPath, plugin);
+    const resolved = await resolver.resolve(repoPath, plugin, options);
 
     // Read clone metadata (written by cloneRepo) so we can pick up the
     // resolved git ref + SHA for manifest recording.
diff --git a/tools/installer/modules/plugin-resolver.js b/tools/installer/modules/plugin-resolver.js
index 7f2a6e06c..25ab6c99e 100644
--- a/tools/installer/modules/plugin-resolver.js
+++ b/tools/installer/modules/plugin-resolver.js
@@ -32,9 +32,15 @@ class PluginResolver {
    * @param {string} [plugin.version] - Semantic version
    * @param {string} [plugin.description] - Plugin description
    * @param {string[]} [plugin.skills] - Relative paths to skill directories
+   * @param {Object} [options] - Resolution options
+   * @param {function} [options.chooseModuleDefinition] - Async selector invoked
+   *   when more than one module.yaml + module-help.csv pair is found between the
+   *   skills' common parent and the repo root. Receives (candidates, context)
+   *   and returns the chosen candidate. When omitted (headless / non-interactive
+   *   / CLI), the deepest candidate is used so resolution never blocks.
    * @returns {Promise<ResolvedModule[]>} Array of resolved module definitions
    */
-  async resolve(repoPath, plugin) {
+  async resolve(repoPath, plugin, options = {}) {
     // Strategy 0: new module system. Tried before everything else — and before
     // the no-skills early return below — because new-system modules declare
     // their skills inside plugin.json rather than via marketplace.json's
@@ -70,7 +76,7 @@ class PluginResolver {
 
     // Try each strategy in order
     const result =
-      (await this._tryRootModuleFiles(repoPath, plugin, skillPaths)) ||
+      (await this._tryRootModuleFiles(repoPath, plugin, skillPaths, options)) ||
       (await this._trySetupSkill(repoPath, plugin, skillPaths)) ||
       (await this._trySingleStandalone(repoPath, plugin, skillPaths)) ||
       (await this._tryMultipleStandalone(repoPath, plugin, skillPaths)) ||
@@ -170,13 +176,38 @@ class PluginResolver {
    * directory that has both files. This catches the common case where, e.g.,
    * module.yaml sits at src/module.yaml but skills are in src/skills/.
    */
-  async _tryRootModuleFiles(repoPath, plugin, skillPaths) {
+  async _tryRootModuleFiles(repoPath, plugin, skillPaths, options = {}) {
     const commonParent = this._computeCommonParent(skillPaths);
-    const found = await this._findModuleFilesUpward(commonParent, repoPath);
-    if (!found) {
+    const candidates = await this._findModuleFileCandidatesUpward(commonParent, repoPath);
+    if (candidates.length === 0) {
       return null;
     }
-    const { moduleYamlPath, moduleHelpPath } = found;
+
+    // Deepest candidate (closest to the skills) is the safe default. When more
+    // than one directory in the chain carries both files, give an interactive
+    // caller the chance to pick — enriching each option with its module.yaml
+    // metadata so the choice is meaningful. Headless callers fall through to
+    // the deepest candidate without prompting.
+    let chosen = candidates[0];
+    if (candidates.length > 1 && typeof options.chooseModuleDefinition === 'function') {
+      const enriched = [];
+      for (const candidate of candidates) {
+        const data = await this._readModuleYaml(candidate.moduleYamlPath);
+        enriched.push({
+          ...candidate,
+          relativePath: path.relative(path.resolve(repoPath), candidate.moduleYamlPath),
+          code: data?.code || null,
+          name: data?.name || null,
+          description: data?.description || null,
+        });
+      }
+      const picked = await options.chooseModuleDefinition(enriched, { plugin });
+      if (picked && picked.moduleYamlPath && picked.moduleHelpPath) {
+        chosen = picked;
+      }
+    }
+
+    const { moduleYamlPath, moduleHelpPath } = chosen;
 
     const moduleData = await this._readModuleYaml(moduleYamlPath);
     if (!moduleData) return null;
@@ -376,14 +407,15 @@ class PluginResolver {
   // ─── Helpers ────────────────────────────────────────────────────────────────
 
   /**
-   * Walk up from startDir to the repo root, returning the first directory that
+   * Walk up from startDir to the repo root, collecting every directory that
    * contains BOTH module.yaml and module-help.csv. Bounded by repoRoot so we
-   * never escape the cloned repository. Returns null if neither pair is found.
+   * never escape the cloned repository. Results are ordered deepest-first
+   * (closest to startDir), so candidates[0] is the safe default.
    * @param {string} startDir - Directory to start searching from (inclusive)
    * @param {string} repoPath - Repository root (upper bound, inclusive)
-   * @returns {Promise<{moduleYamlPath: string, moduleHelpPath: string}|null>}
+   * @returns {Promise<Array<{moduleYamlPath: string, moduleHelpPath: string}>>}
    */
-  async _findModuleFilesUpward(startDir, repoPath) {
+  async _findModuleFileCandidatesUpward(startDir, repoPath) {
     const repoRoot = path.resolve(repoPath);
     let dir = path.resolve(startDir);
 
@@ -392,11 +424,12 @@ class PluginResolver {
       dir = repoRoot;
     }
 
+    const candidates = [];
     while (true) {
       const moduleYamlPath = path.join(dir, 'module.yaml');
       const moduleHelpPath = path.join(dir, 'module-help.csv');
       if ((await fs.pathExists(moduleYamlPath)) && (await fs.pathExists(moduleHelpPath))) {
-        return { moduleYamlPath, moduleHelpPath };
+        candidates.push({ moduleYamlPath, moduleHelpPath });
       }
       if (dir === repoRoot) break;
       const parent = path.dirname(dir);
@@ -404,7 +437,7 @@ class PluginResolver {
       dir = parent;
     }
 
-    return null;
+    return candidates;
   }
 
   /**
diff --git a/tools/installer/ui.js b/tools/installer/ui.js
index 2a520144f..810f6be90 100644
--- a/tools/installer/ui.js
+++ b/tools/installer/ui.js
@@ -1008,6 +1008,25 @@ class UI {
     const customMgr = new CustomModuleManager();
     const selectedModules = [];
 
+    // Interactive disambiguation: when a plugin has more than one module.yaml +
+    // module-help.csv pair between its skills and the repo root, let the user
+    // pick which one defines the module. `activeSpinner` is paused around the
+    // prompt so the choice renders cleanly, then resumed by the caller.
+    let activeSpinner = null;
+    const chooseModuleDefinition = async (candidates, { plugin }) => {
+      activeSpinner?.stop('Multiple module definitions found');
+      const choice = await prompts.select({
+        message: `"${plugin.name}" declares multiple module definitions — choose which to install:`,
+        choices: candidates.map((c) => ({
+          name: `${c.code || '(no code)'}${c.name ? ` — ${c.name}` : ''}  [${c.relativePath}]`,
+          value: c,
+        })),
+        default: candidates[0],
+      });
+      activeSpinner?.start('Analyzing plugin structure...');
+      return choice;
+    };
+
     let addMore = true;
     while (addMore) {
       const sourceInput = await prompts.text({
@@ -1021,6 +1040,7 @@ class UI {
       });
 
       const s = await prompts.spinner();
+      activeSpinner = s;
       s.start('Resolving source...');
 
       let sourceResult;
@@ -1062,7 +1082,9 @@ class UI {
         const effectiveRepoPath = sourceResult.repoPath || sourceResult.rootDir;
         for (const plugin of plugins) {
           try {
-            const resolved = await customMgr.resolvePlugin(effectiveRepoPath, plugin.rawPlugin, sourceResult.sourceUrl, localPath);
+            const resolved = await customMgr.resolvePlugin(effectiveRepoPath, plugin.rawPlugin, sourceResult.sourceUrl, localPath, {
+              chooseModuleDefinition,
+            });
             if (resolved.length > 0) {
               allResolved.push(...resolved);
             } else {
@@ -1117,7 +1139,9 @@ class UI {
         // so an empty skills[] here is expected); legacy modules need ≥1 skill.
         if (rootManifest || directPlugin.skills.length > 0) {
           try {
-            const resolved = await customMgr.resolvePlugin(sourceResult.rootDir, directPlugin, sourceResult.sourceUrl, localPath);
+            const resolved = await customMgr.resolvePlugin(sourceResult.rootDir, directPlugin, sourceResult.sourceUrl, localPath, {
+              chooseModuleDefinition,
+            });
             allResolved.push(...resolved);
           } catch (resolveError) {
             await prompts.log.warn(`  Could not resolve: ${resolveError.message}`);