diff --git a/packages/sync-engine/src/supabase/supabase.test.ts b/packages/sync-engine/src/supabase/supabase.test.ts
index 12a74bfb..4a9b507c 100644
--- a/packages/sync-engine/src/supabase/supabase.test.ts
+++ b/packages/sync-engine/src/supabase/supabase.test.ts
@@ -474,6 +474,57 @@ describe('SupabaseDeployClient', () => {
       }
     })
 
+    it('should return false when uninstallation is in progress (uninstallation:started)', async () => {
+      const client = new SupabaseSetupClient({
+        accessToken: mockAccessToken,
+        projectRef: mockProjectRef,
+      })
+
+      // Mock runSQL to return in-progress uninstallation
+      const mockRunSQL = vi
+        .fn()
+        .mockResolvedValueOnce([{ rows: [{ schema_exists: true }] }]) // schema exists
+        .mockResolvedValueOnce([{ rows: [{ table_exists: true }] }]) // migrations table exists
+        .mockResolvedValueOnce([
+          { rows: [{ comment: 'stripe-sync v1.0.0 uninstallation:started' }] },
+        ]) // in progress
+      // @ts-expect-error - accessing private method for testing
+      client.runSQL = mockRunSQL
+
+      const installed = await client.isInstalled()
+
+      expect(installed).toBe(false)
+    })
+
+    it('should throw error when uninstallation has failed (uninstallation:error)', async () => {
+      const client = new SupabaseSetupClient({
+        accessToken: mockAccessToken,
+        projectRef: mockProjectRef,
+      })
+
+      // Mock runSQL to return failed uninstallation
+      const mockRunSQL = vi
+        .fn()
+        .mockResolvedValueOnce([{ rows: [{ schema_exists: true }] }]) // schema exists
+        .mockResolvedValueOnce([{ rows: [{ table_exists: true }] }]) // migrations table exists
+        .mockResolvedValueOnce([
+          {
+            rows: [{ comment: 'stripe-sync v1.0.0 uninstallation:error - Cleanup failed' }],
+          },
+        ]) // failed
+      // @ts-expect-error - accessing private method for testing
+      client.runSQL = mockRunSQL
+
+      try {
+        await client.isInstalled()
+        expect.fail('Should have thrown an error')
+      } catch (error) {
+        expect(error).toBeInstanceOf(Error)
+        expect((error as Error).message).toContain('Uninstallation failed')
+        expect((error as Error).message).toContain('Manual cleanup may be required')
+      }
+    })
+
     it('should return true when installation is complete', async () => {
       const client = new SupabaseSetupClient({
         accessToken: mockAccessToken,
diff --git a/packages/sync-engine/src/supabase/supabase.ts b/packages/sync-engine/src/supabase/supabase.ts
index 71595c2b..fac924af 100644
--- a/packages/sync-engine/src/supabase/supabase.ts
+++ b/packages/sync-engine/src/supabase/supabase.ts
@@ -11,6 +11,8 @@ export const STRIPE_SCHEMA_COMMENT_PREFIX = 'stripe-sync'
 export const INSTALLATION_STARTED_SUFFIX = 'installation:started'
 export const INSTALLATION_ERROR_SUFFIX = 'installation:error'
 export const INSTALLATION_INSTALLED_SUFFIX = 'installed'
+export const UNINSTALLATION_STARTED_SUFFIX = 'uninstallation:started'
+export const UNINSTALLATION_ERROR_SUFFIX = 'uninstallation:error'
 
 export interface DeployClientOptions {
   accessToken: string
@@ -310,6 +312,27 @@ export class SupabaseSetupClient {
     return { success: true }
   }
 
+  /**
+   * Check if a schema exists in the database
+   * @param schema The schema name to check (defaults to 'stripe')
+   * @returns true if schema exists, false otherwise
+   */
+  private async schemaExists(schema = 'stripe'): Promise<boolean> {
+    try {
+      const schemaCheck = (await this.runSQL(
+        `SELECT EXISTS (
+          SELECT 1 FROM information_schema.schemata
+          WHERE schema_name = '${schema}'
+        ) as schema_exists`
+      )) as { rows?: { schema_exists: boolean }[] }[]
+
+      return schemaCheck[0]?.rows?.[0]?.schema_exists === true
+    } catch {
+      // Return false if query fails
+      return false
+    }
+  }
+
   /**
    * Check if stripe-sync is installed in the database.
    *
@@ -324,16 +347,9 @@ export class SupabaseSetupClient {
   async isInstalled(schema = 'stripe'): Promise<boolean> {
     try {
       // Step 1: Duck typing - check if schema exists
-      const schemaCheck = (await this.runSQL(
-        `SELECT EXISTS (
-          SELECT 1 FROM information_schema.schemata
-          WHERE schema_name = '${schema}'
-        ) as schema_exists`
-      )) as { rows?: { schema_exists: boolean }[] }[]
+      const schemaExistsResult = await this.schemaExists(schema)
 
-      const schemaExists = schemaCheck[0]?.rows?.[0]?.schema_exists === true
-
-      if (!schemaExists) {
+      if (!schemaExistsResult) {
         // Schema doesn't exist - not installed
         return false
       }
@@ -371,6 +387,20 @@ export class SupabaseSetupClient {
         )
       }
 
+      // Check for uninstallation in progress
+      // NOTE: Check uninstallation before installation since "uninstallation:*" contains "installation:*"
+      if (comment.includes(UNINSTALLATION_STARTED_SUFFIX)) {
+        return false
+      }
+
+      // Check for failed uninstallation (requires manual intervention)
+      if (comment.includes(UNINSTALLATION_ERROR_SUFFIX)) {
+        throw new Error(
+          `Uninstallation failed: Schema '${schema}' exists but uninstallation encountered an error. ` +
+            `Comment: ${comment}. Manual cleanup may be required.`
+        )
+      }
+
       // Check for incomplete installation (can retry)
       if (comment.includes(INSTALLATION_STARTED_SUFFIX)) {
         return false
@@ -391,7 +421,8 @@ export class SupabaseSetupClient {
       if (
         error instanceof Error &&
         (error.message.includes('Legacy installation detected') ||
-          error.message.includes('Installation failed'))
+          error.message.includes('Installation failed') ||
+          error.message.includes('Uninstallation failed'))
       ) {
         throw error
       }
@@ -435,9 +466,18 @@ export class SupabaseSetupClient {
   /**
    * Uninstall stripe-sync from a Supabase project
    * Invokes the stripe-setup edge function's DELETE endpoint which handles cleanup
+   * Tracks uninstallation progress via schema comments
    */
   async uninstall(): Promise<void> {
     try {
+      // Check if schema exists and mark uninstall as started
+      const hasSchema = await this.schemaExists('stripe')
+      if (hasSchema) {
+        await this.updateInstallationComment(
+          `${STRIPE_SCHEMA_COMMENT_PREFIX} v${pkg.version} ${UNINSTALLATION_STARTED_SUFFIX}`
+        )
+      }
+
       // Invoke the DELETE endpoint on stripe-setup function
       // Use accessToken in Authorization header for Management API validation
       const url = `https://${this.projectRef}.${this.projectBaseUrl}/functions/v1/stripe-setup`
@@ -458,7 +498,23 @@ export class SupabaseSetupClient {
       if (result.success === false) {
         throw new Error(`Uninstall failed: ${result.error}`)
       }
+      // On success, schema is dropped by edge function (no comment update needed)
     } catch (error) {
+      // Mark schema with error if it still exists
+      try {
+        const hasSchema = await this.schemaExists('stripe')
+        if (hasSchema) {
+          await this.updateInstallationComment(
+            `${STRIPE_SCHEMA_COMMENT_PREFIX} v${pkg.version} ${UNINSTALLATION_ERROR_SUFFIX} - ${
+              error instanceof Error ? error.message : String(error)
+            }`
+          )
+        }
+      } catch (error) {
+        throw new Error(
+          `Uninstall failed: ${error instanceof Error ? error.message : String(error)}`
+        )
+      }
       throw new Error(`Uninstall failed: ${error instanceof Error ? error.message : String(error)}`)
     }
   }