diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c6527e..8a5f944 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to the "promptitude" extension will be documented in this fi
 
 ## [Unreleased]
 
+### Added
+
+- Prompt size safeguard: warns when active prompts may overwhelm GitHub Copilot's context window. Checks total file size (>500 KB), active prompt count (>50), and repository count (>10) after each sync. Shows actionable warning with "Manage Prompts" and "Open Settings" buttons.
+- Disabled (inactive) prompts are now cleaned up from the active prompts directory during sync, preventing them from being loaded by Copilot.
+
 ## [1.5.4] - 2026-01-12
 
 ### Fixed
diff --git a/src/constant.ts b/src/constant.ts
index b5f9830..e750bb5 100644
--- a/src/constant.ts
+++ b/src/constant.ts
@@ -4,3 +4,11 @@ export const REPO_SYNC_CHAT_MODE_LEGACY_PATH = `chatmodes/`;
 export const REPO_SYNC_CHAT_MODE_LEGACY_SINGULAR_PATH = `chatmode/`;
 export const REPO_SYNC_INSTRUCTIONS_PATH = `instructions/`;
 export const REPO_SYNC_PROMPT_PATH = `prompts/`;
+
+// Prompt size safeguard thresholds
+/** Maximum total size (in bytes) of all active prompts before warning the user */
+export const PROMPT_SIZE_WARNING_THRESHOLD_BYTES = 500 * 1024; // 500 KB
+/** Maximum number of active prompts before warning the user */
+export const PROMPT_COUNT_WARNING_THRESHOLD = 50;
+/** Maximum number of configured repositories before warning the user */
+export const REPO_COUNT_WARNING_THRESHOLD = 10;
diff --git a/src/syncManager.ts b/src/syncManager.ts
index 0231894..0e90730 100644
--- a/src/syncManager.ts
+++ b/src/syncManager.ts
@@ -10,7 +10,7 @@ import { GitProviderFactory } from './utils/gitProviderFactory';
 import { FileSystemManager } from './utils/fileSystem';
 import { AzureDevOpsApiManager } from './utils/azureDevOps';
 import { PromptTreeDataProvider } from './ui/promptTreeProvider';
-import { 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, } from './constant';
+import { 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, PROMPT_SIZE_WARNING_THRESHOLD_BYTES, PROMPT_COUNT_WARNING_THRESHOLD, REPO_COUNT_WARNING_THRESHOLD, } from './constant';
 export interface SyncResult {
     success: boolean;
     itemsUpdated: number;
@@ -102,12 +102,18 @@ export class SyncManager {
             // Recreate symlinks for active prompts (in case they were manually deleted)
             await this.recreateActivePromptSymlinks();
 
+            // Remove disabled prompts from the active prompts directory
+            await this.cleanupInactivePrompts();
+
             // Clean up orphaned regular files in prompts directory
             const cleanup = await this.cleanupOrphanedPrompts();
             if (cleanup.removed > 0) {
                 this.logger.info(`Cleaned up ${cleanup.removed} orphaned prompt files`);
             }
 
+            // Validate total prompt size to prevent Copilot context overflow
+            await this.validatePromptSize();
+
             // Update status based on overall result
             if (result.overallSuccess) {
                 this.statusBar.setStatus(SyncStatus.Success);
@@ -1226,6 +1232,66 @@ export class SyncManager {
         }
     }
 
+    /**
+     * Validate total prompt size and count, warning the user if thresholds are exceeded.
+     * This prevents GitHub Copilot's context window from being overwhelmed.
+     */
+    private async validatePromptSize(): Promise<void> {
+        try {
+            const fs = require('fs').promises;
+            const promptsDir = this.config.getPromptsDirectory();
+
+            // Ensure the prompts directory exists
+            await this.fileSystem.ensureDirectoryExists(promptsDir);
+
+            const entries = await this.fileSystem.readDirectory(promptsDir);
+            const promptFiles = entries.filter(f => this.isPromptFile(f));
+
+            // Calculate total size of active prompt files
+            let totalSize = 0;
+            let activeCount = 0;
+
+            for (const file of promptFiles) {
+                try {
+                    const filePath = this.fileSystem.joinPath(promptsDir, file);
+                    const stats = await fs.stat(filePath);
+                    totalSize += stats.size;
+                    activeCount++;
+                } catch {
+                    // Skip files that can't be stat'd
+                }
+            }
+
+            const repoCount = this.config.repositories.length;
+            const totalSizeKB = totalSize / 1024;
+            const reasons: string[] = [];
+
+            if (totalSize > PROMPT_SIZE_WARNING_THRESHOLD_BYTES) {
+                reasons.push(`total size (${totalSizeKB.toFixed(0)} KB) exceeds ${(PROMPT_SIZE_WARNING_THRESHOLD_BYTES / 1024).toFixed(0)} KB`);
+            }
+            if (activeCount > PROMPT_COUNT_WARNING_THRESHOLD) {
+                reasons.push(`${activeCount} active prompts exceeds limit of ${PROMPT_COUNT_WARNING_THRESHOLD}`);
+            }
+            if (repoCount > REPO_COUNT_WARNING_THRESHOLD) {
+                reasons.push(`${repoCount} repositories exceeds limit of ${REPO_COUNT_WARNING_THRESHOLD}`);
+            }
+
+            if (reasons.length > 0) {
+                this.logger.warn(`Prompt size safeguard triggered: ${reasons.join('; ')}`);
+                await this.notifications.showPromptSizeWarning({
+                    totalSizeKB,
+                    activeCount,
+                    repoCount,
+                    reasons
+                });
+            } else {
+                this.logger.debug(`Prompt size check passed: ${activeCount} prompts, ${totalSizeKB.toFixed(1)} KB, ${repoCount} repos`);
+            }
+        } catch (error) {
+            this.logger.error('Failed to validate prompt size', error instanceof Error ? error : undefined);
+        }
+    }
+
     dispose(): void {
         this.logger.info('Disposing SyncManager...');
 
diff --git a/src/utils/notifications.ts b/src/utils/notifications.ts
index 2340c07..2180a59 100644
--- a/src/utils/notifications.ts
+++ b/src/utils/notifications.ts
@@ -162,4 +162,27 @@ export class NotificationManager {
             await this.showError(`Failed to setup Azure DevOps authentication: ${errorMessage}`);
         }
     }
+
+    /**
+     * Show a warning when the total prompt size or count exceeds safe thresholds.
+     * Always shown regardless of showNotifications setting to prevent Copilot context overflow.
+     */
+    async showPromptSizeWarning(details: { totalSizeKB: number; activeCount: number; repoCount: number; reasons: string[] }): Promise<void> {
+        const reasonText = details.reasons.join('; ');
+        const message = `⚠️ Promptitude: Your active prompts may be too large for GitHub Copilot (${details.totalSizeKB.toFixed(0)} KB across ${details.activeCount} prompts from ${details.repoCount} repos). ${reasonText}. Consider disabling unused prompts, reducing synced repositories, or switching to manual sync.`;
+
+        // Always show this warning regardless of notification settings — it's a safeguard
+        const result = await vscode.window.showWarningMessage(
+            message,
+            'Manage Prompts',
+            'Open Settings',
+            'Dismiss'
+        );
+
+        if (result === 'Manage Prompts') {
+            vscode.commands.executeCommand('promptitude-prompts.focus');
+        } else if (result === 'Open Settings') {
+            vscode.commands.executeCommand('workbench.action.openSettings', 'promptitude');
+        }
+    }
 }