diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c6527e..1371747 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to the "promptitude" extension will be documented in this fi
 
 ## [Unreleased]
 
+### Improved
+
+- Sync failure messages now distinguish **invalid repository URLs** (e.g. sub-paths like `/tree/main/...`) from **incompatible repository structures** (repo is reachable but has no supported prompt folders). The summary toast shows a categorised count, and "Show Details" lists the specific reason per repository.
+
 ## [1.5.4] - 2026-01-12
 
 ### Fixed
diff --git a/src/syncManager.ts b/src/syncManager.ts
index 0231894..d1dc1f8 100644
--- a/src/syncManager.ts
+++ b/src/syncManager.ts
@@ -325,6 +325,27 @@ export class SyncManager {
         }
     }
 
+    /**
+     * Validates that a repository URL is a well-formed repo root (not a sub-path like /tree/main/...).
+     * Returns an error string if invalid, or undefined if valid.
+     */
+    private validateRepositoryUrl(repoUrl: string): string | undefined {
+        try {
+            const parsed = new URL(repoUrl);
+            const normalizedPath = parsed.pathname.replace(/\.git$/, '').replace(/\/+$/, '');
+            const segments = normalizedPath.split('/').filter(Boolean);
+
+            // GitHub: expect exactly owner/repo (2 segments)
+            if (parsed.hostname === 'github.com' && segments.length !== 2) {
+                return `Invalid URL – expected https://github.com/owner/repo but got a sub-path (${parsed.pathname}). Remove extra path segments like /tree/…`;
+            }
+
+            return undefined;
+        } catch {
+            return `Invalid URL format – could not parse "${repoUrl}" as a repository URL`;
+        }
+    }
+
     private async syncMultipleRepositories(repositories: string[]): Promise<MultiRepositorySyncResult> {
         const results: RepositorySyncResult[] = [];
         let totalItemsUpdated = 0;
@@ -338,6 +359,20 @@ export class SyncManager {
             try {
                 this.logger.debug(`Syncing repository: ${repoUrl}`);
 
+                // Early validation: reject malformed repository URLs
+                const urlError = this.validateRepositoryUrl(repoUrl);
+                if (urlError) {
+                    this.logger.warn(`Skipping repository ${repoUrl}: ${urlError}`);
+                    results.push({
+                        repository: repoUrl,
+                        success: false,
+                        itemsUpdated: 0,
+                        error: urlError
+                    });
+                    errors.push(`${repoUrl}: ${urlError}`);
+                    continue;
+                }
+
                 // Get or create Git API manager for this repository
                 let gitApi = this.gitProviders.get(repoUrl);
                 if (!gitApi) {
@@ -379,14 +414,20 @@ export class SyncManager {
 
                 if (relevantFiles.length === 0) {
                     this.logger.warn(`No relevant files found to sync in ${repoUrl} based on current settings`);
-                    const promptLocation = `${REPO_SYNC_CHAT_MODE_PATH}, ${REPO_SYNC_CHAT_MODE_LEGACY_PATH}, ${REPO_SYNC_CHAT_MODE_LEGACY_SINGULAR_PATH}, ${REPO_SYNC_INSTRUCTIONS_PATH}, ${REPO_SYNC_PROMPT_PATH}`;
+                    const enabledTypes: string[] = [];
+                    if (this.config.syncChatmode) { enabledTypes.push(REPO_SYNC_CHAT_MODE_PATH); }
+                    if (this.config.syncInstructions) { enabledTypes.push(REPO_SYNC_INSTRUCTIONS_PATH); }
+                    if (this.config.syncPrompt) { enabledTypes.push(REPO_SYNC_PROMPT_PATH); }
+                    const structureError = enabledTypes.length > 0
+                        ? `Incompatible repository – no .md/.txt files found under ${enabledTypes.join(', ')} on branch "${branch}". Check that the repo uses a supported folder layout.`
+                        : `No sync types enabled – enable at least one of syncChatmode, syncInstructions, or syncPrompt in settings.`;
                     results.push({
                         repository: repoUrl,
                         success: false,
                         itemsUpdated: 0,
-                        error: `No relevant files found, make sure prompts are in valid directories: ${promptLocation}`
+                        error: structureError
                     });
-                    errors.push(`${repoUrl}: No relevant files found`);
+                    errors.push(`${repoUrl}: ${structureError}`);
                     continue;
                 }
                 this.logger.debug(`Found ${relevantFiles.length} relevant files to sync for ${repoUrl}`);
diff --git a/src/utils/notifications.ts b/src/utils/notifications.ts
index 2340c07..5af899d 100644
--- a/src/utils/notifications.ts
+++ b/src/utils/notifications.ts
@@ -47,7 +47,27 @@ export class NotificationManager {
     }
 
     async showPartialSyncSuccess(itemsCount: number, successCount: number, totalCount: number, errors: string[]): Promise<void> {
-        const message = `⚠️ Partial sync completed! ${itemsCount} items updated from ${successCount}/${totalCount} repositories.`;
+        // Categorise failures so the summary toast is immediately actionable
+        let badUrlCount = 0;
+        let badStructureCount = 0;
+        let otherCount = 0;
+        for (const err of errors) {
+            if (err.includes('Invalid URL')) {
+                badUrlCount++;
+            } else if (err.includes('Incompatible repository') || err.includes('No sync types enabled')) {
+                badStructureCount++;
+            } else {
+                otherCount++;
+            }
+        }
+
+        const failParts: string[] = [];
+        if (badUrlCount > 0) { failParts.push(`${badUrlCount} bad URL${badUrlCount > 1 ? 's' : ''}`); }
+        if (badStructureCount > 0) { failParts.push(`${badStructureCount} incompatible structure`); }
+        if (otherCount > 0) { failParts.push(`${otherCount} other error${otherCount > 1 ? 's' : ''}`); }
+
+        const failSummary = failParts.length > 0 ? ` Failures: ${failParts.join(', ')}.` : '';
+        const message = `⚠️ Partial sync: ${itemsCount} items updated from ${successCount}/${totalCount} repos.${failSummary}`;
         const result = await this.showWarning(
             message,
             'Show Details',