diff --git a/web/src/server/pty/pty-manager.ts b/web/src/server/pty/pty-manager.ts
index 4fef2bfa..b17d1939 100644
--- a/web/src/server/pty/pty-manager.ts
+++ b/web/src/server/pty/pty-manager.ts
@@ -32,6 +32,7 @@ import {
   shouldInjectTitle,
 } from '../utils/terminal-title.js';
 import { WriteQueue } from '../utils/write-queue.js';
+import { VERSION } from '../version.js';
 import { AsciinemaWriter } from './asciinema-writer.js';
 import { ProcessUtils } from './process-utils.js';
 import { SessionManager } from './session-manager.js';
@@ -244,6 +245,7 @@ export class PtyManager extends EventEmitter {
         startedAt: new Date().toISOString(),
         initialCols: cols,
         initialRows: rows,
+        version: VERSION,
       };
 
       // Save initial session info
diff --git a/web/src/server/pty/session-manager.ts b/web/src/server/pty/session-manager.ts
index 71287ea4..43db3e63 100644
--- a/web/src/server/pty/session-manager.ts
+++ b/web/src/server/pty/session-manager.ts
@@ -12,6 +12,7 @@ import * as os from 'os';
 import * as path from 'path';
 import type { Session, SessionInfo } from '../../shared/types.js';
 import { createLogger } from '../utils/logger.js';
+import { VERSION } from '../version.js';
 import { ProcessUtils } from './process-utils.js';
 import { PtyError } from './types.js';
 
@@ -49,6 +50,44 @@ export class SessionManager {
     }
   }
 
+  /**
+   * Get the path to the version tracking file
+   */
+  private getVersionFilePath(): string {
+    return path.join(this.controlPath, '.version');
+  }
+
+  /**
+   * Read the last known version from the version file
+   */
+  private readLastVersion(): string | null {
+    try {
+      const versionFile = this.getVersionFilePath();
+      if (fs.existsSync(versionFile)) {
+        const content = fs.readFileSync(versionFile, 'utf8').trim();
+        logger.debug(`read last version from file: ${content}`);
+        return content;
+      }
+      return null;
+    } catch (error) {
+      logger.warn(`failed to read version file: ${error}`);
+      return null;
+    }
+  }
+
+  /**
+   * Write the current version to the version file
+   */
+  private writeCurrentVersion(): void {
+    try {
+      const versionFile = this.getVersionFilePath();
+      fs.writeFileSync(versionFile, VERSION, 'utf8');
+      logger.debug(`wrote current version to file: ${VERSION}`);
+    } catch (error) {
+      logger.warn(`failed to write version file: ${error}`);
+    }
+  }
+
   /**
    * Create a new session directory structure
    */
@@ -396,6 +435,76 @@ export class SessionManager {
     }
   }
 
+  /**
+   * Cleanup sessions from old VibeTunnel versions
+   * This is called during server startup to clean sessions when version changes
+   */
+  cleanupOldVersionSessions(): { versionChanged: boolean; cleanedCount: number } {
+    const lastVersion = this.readLastVersion();
+    const currentVersion = VERSION;
+
+    // If no version file exists, this is likely a fresh install or first time with version tracking
+    if (!lastVersion) {
+      logger.debug('no previous version found, checking for legacy sessions');
+
+      // Clean up any sessions without version field
+      let cleanedCount = 0;
+      const sessions = this.listSessions();
+      for (const session of sessions) {
+        if (!session.version) {
+          logger.debug(`cleaning up legacy session ${session.id} (no version field)`);
+          this.cleanupSession(session.id);
+          cleanedCount++;
+        }
+      }
+
+      this.writeCurrentVersion();
+      return { versionChanged: false, cleanedCount };
+    }
+
+    // If version hasn't changed, nothing to do
+    if (lastVersion === currentVersion) {
+      logger.debug(`version unchanged (${currentVersion}), skipping cleanup`);
+      return { versionChanged: false, cleanedCount: 0 };
+    }
+
+    logger.log(chalk.yellow(`VibeTunnel version changed from ${lastVersion} to ${currentVersion}`));
+    logger.log(chalk.yellow('cleaning up old sessions...'));
+
+    let cleanedCount = 0;
+    try {
+      const sessions = this.listSessions();
+
+      for (const session of sessions) {
+        // Clean all sessions that don't match the current version
+        // Sessions without version field are considered old
+        if (!session.version || session.version !== currentVersion) {
+          logger.debug(
+            `cleaning up session ${session.id} (version: ${session.version || 'unknown'})`
+          );
+          this.cleanupSession(session.id);
+          cleanedCount++;
+        }
+      }
+
+      // Update the version file to current version
+      this.writeCurrentVersion();
+
+      if (cleanedCount > 0) {
+        logger.log(chalk.green(`cleaned up ${cleanedCount} sessions from previous version`));
+      } else {
+        logger.log(chalk.gray('no old sessions to clean up'));
+      }
+
+      return { versionChanged: true, cleanedCount };
+    } catch (error) {
+      logger.error(`failed to cleanup old version sessions: ${error}`);
+      // Still update version file to prevent repeated cleanup attempts
+      this.writeCurrentVersion();
+      return { versionChanged: true, cleanedCount };
+    }
+  }
+
   /**
    * Get session paths for a given session ID
    */
diff --git a/web/src/server/server.ts b/web/src/server/server.ts
index a9ddbaf5..1fefaf85 100644
--- a/web/src/server/server.ts
+++ b/web/src/server/server.ts
@@ -396,6 +396,23 @@ export async function createApp(): Promise<AppInstance> {
   const ptyManager = new PtyManager(CONTROL_DIR);
   logger.debug('Initialized PTY manager');
 
+  // Clean up sessions from old VibeTunnel versions
+  const sessionManager = ptyManager.getSessionManager();
+  const cleanupResult = sessionManager.cleanupOldVersionSessions();
+  if (cleanupResult.versionChanged) {
+    logger.log(
+      chalk.yellow(
+        `Version change detected - cleaned up ${cleanupResult.cleanedCount} sessions from previous version`
+      )
+    );
+  } else if (cleanupResult.cleanedCount > 0) {
+    logger.log(
+      chalk.yellow(
+        `Cleaned up ${cleanupResult.cleanedCount} legacy sessions without version information`
+      )
+    );
+  }
+
   // Initialize Terminal Manager for server-side terminal state
   const terminalManager = new TerminalManager(CONTROL_DIR);
   logger.debug('Initialized terminal manager');
diff --git a/web/src/shared/types.ts b/web/src/shared/types.ts
index 78421184..d867eabe 100644
--- a/web/src/shared/types.ts
+++ b/web/src/shared/types.ts
@@ -22,6 +22,7 @@ export interface SessionInfo {
   pid?: number;
   initialCols?: number;
   initialRows?: number;
+  version?: string; // VibeTunnel version that created this session
 }
 
 /**