diff --git a/tools/common/lib/sqlite-integration.ts b/tools/common/lib/sqlite-integration.ts
index a4c8205978..f42a908a6a 100644
--- a/tools/common/lib/sqlite-integration.ts
+++ b/tools/common/lib/sqlite-integration.ts
@@ -19,6 +19,20 @@ export abstract class SqliteIntegrationProvider {
 		return hasDbPhp || ! hasWpConfig;
 	}
 
+	async shouldKeepExistingDbDropin( sitePath: string ): Promise< boolean > {
+		const dbPhpPath = path.join( sitePath, 'wp-content', 'db.php' );
+		if ( ! fs.existsSync( dbPhpPath ) ) {
+			return false;
+		}
+
+		try {
+			const content = await fs.promises.readFile( dbPhpPath, 'utf8' );
+			return content.includes( '@studio-keep' );
+		} catch {
+			return false;
+		}
+	}
+
 	async getSqliteVersionFromInstallation( sqliteMuPluginPath: string ): Promise< string > {
 		try {
 			const versionFileContent = await fs.promises.readFile(
@@ -39,20 +53,22 @@ export abstract class SqliteIntegrationProvider {
 
 		const wpContentPath = path.join( sitePath, 'wp-content' );
 		const databasePath = path.join( wpContentPath, 'database' );
+		const sqliteSourcePath = this.getSqlitePluginSourcePath();
+		const sqliteDirname = this.getSqliteDirname();
 
 		await fs.promises.mkdir( databasePath, { recursive: true } );
 
-		const sqliteSourcePath = this.getSqlitePluginSourcePath();
-		const dbCopyContent = await fs.promises.readFile(
-			path.join( sqliteSourcePath, 'db.copy' ),
-			'utf8'
-		);
-		const sqliteDirname = this.getSqliteDirname();
-		const updatedContent = dbCopyContent.replace(
-			"'{SQLITE_IMPLEMENTATION_FOLDER_PATH}'",
-			`realpath( __DIR__ . '/mu-plugins/${ sqliteDirname }' )`
-		);
-		await fs.promises.writeFile( path.join( wpContentPath, 'db.php' ), updatedContent );
+		if ( ! ( await this.shouldKeepExistingDbDropin( sitePath ) ) ) {
+			const dbCopyContent = await fs.promises.readFile(
+				path.join( sqliteSourcePath, 'db.copy' ),
+				'utf8'
+			);
+			const updatedContent = dbCopyContent.replace(
+				"'{SQLITE_IMPLEMENTATION_FOLDER_PATH}'",
+				`realpath( __DIR__ . '/mu-plugins/${ sqliteDirname }' )`
+			);
+			await fs.promises.writeFile( path.join( wpContentPath, 'db.php' ), updatedContent );
+		}
 
 		const sqliteDestPath = path.join( wpContentPath, 'mu-plugins', sqliteDirname );
 		await fs.promises.rm( sqliteDestPath, { recursive: true, force: true } );
diff --git a/tools/common/lib/tests/sqlite-integration.test.ts b/tools/common/lib/tests/sqlite-integration.test.ts
index c270a53396..d564be814d 100644
--- a/tools/common/lib/tests/sqlite-integration.test.ts
+++ b/tools/common/lib/tests/sqlite-integration.test.ts
@@ -83,6 +83,33 @@ platformTestSuite( 'SqliteIntegrationProvider', ( { normalize } ) => {
 		} );
 	} );
 
+	describe( 'shouldKeepExistingDbDropin', () => {
+		it( 'should return false when db.php does not exist', async () => {
+			const result = await provider.shouldKeepExistingDbDropin( MOCK_SITE_PATH );
+			expect( result ).toBe( false );
+		} );
+
+		it( 'should return false when db.php does not include the Studio keep marker', async () => {
+			volFromJSON( {
+				[ normalize( `${ MOCK_SITE_PATH }/wp-content/db.php` ) ]:
+					"<?php\ndefine( 'SQLITE_DB_DROPIN_VERSION', '1.8.0' );\ndefine( 'MARKDOWN_DB_DROPIN', true );",
+			} );
+
+			const result = await provider.shouldKeepExistingDbDropin( MOCK_SITE_PATH );
+			expect( result ).toBe( false );
+		} );
+
+		it( 'should return true when db.php includes the Studio keep marker', async () => {
+			volFromJSON( {
+				[ normalize( `${ MOCK_SITE_PATH }/wp-content/db.php` ) ]:
+					"<?php\n// @studio-keep\ndefine( 'SQLITE_DB_DROPIN_VERSION', '1.8.0' );\ndefine( 'MARKDOWN_DB_DROPIN', true );",
+			} );
+
+			const result = await provider.shouldKeepExistingDbDropin( MOCK_SITE_PATH );
+			expect( result ).toBe( true );
+		} );
+	} );
+
 	describe( 'installSqliteIntegration', () => {
 		beforeEach( () => {
 			volFromJSON( {
@@ -109,6 +136,39 @@ platformTestSuite( 'SqliteIntegrationProvider', ( { normalize } ) => {
 			);
 		} );
 
+		it( 'should not overwrite db.php drop-in with the Studio keep marker', async () => {
+			volFromJSON( {
+				[ normalize( `wp-files/${ SQLITE_DIRNAME }/db.copy` ) ]:
+					"SQLIntegration path: '{SQLITE_IMPLEMENTATION_FOLDER_PATH}'",
+				[ normalize( `${ MOCK_SITE_PATH }/wp-content/db.php` ) ]:
+					"<?php\n// @studio-keep\ndefine( 'SQLITE_DB_DROPIN_VERSION', '1.8.0' );\ndefine( 'MARKDOWN_DB_DROPIN', true );",
+			} );
+
+			await provider.installSqliteIntegration( MOCK_SITE_PATH );
+
+			expect( vi.mocked( fs.promises.writeFile ) ).not.toHaveBeenCalledWith(
+				normalize( `${ MOCK_SITE_PATH }/wp-content/db.php` ),
+				expect.any( String )
+			);
+		} );
+
+		it( 'should still copy mu-plugin when db.php has the Studio keep marker', async () => {
+			volFromJSON( {
+				[ normalize( `wp-files/${ SQLITE_DIRNAME }/db.copy` ) ]:
+					"SQLIntegration path: '{SQLITE_IMPLEMENTATION_FOLDER_PATH}'",
+				[ normalize( `${ MOCK_SITE_PATH }/wp-content/db.php` ) ]:
+					"<?php\n// @studio-keep\ndefine( 'SQLITE_DB_DROPIN_VERSION', '1.8.0' );\ndefine( 'MARKDOWN_DB_DROPIN', true );",
+			} );
+
+			await provider.installSqliteIntegration( MOCK_SITE_PATH );
+
+			expect( vi.mocked( fs.promises.cp ) ).toHaveBeenCalledWith(
+				normalize( `wp-files/${ SQLITE_DIRNAME }` ),
+				normalize( `${ MOCK_SITE_PATH }/wp-content/mu-plugins/${ SQLITE_DIRNAME }` ),
+				expect.any( Object )
+			);
+		} );
+
 		it( 'should copy SQLite plugin to mu-plugins', async () => {
 			await provider.installSqliteIntegration( MOCK_SITE_PATH );