diff --git a/apps/cli/commands/tests/import.e2e.test.ts b/apps/cli/commands/tests/import.e2e.test.ts
index c808546820..a1b6d8c184 100644
--- a/apps/cli/commands/tests/import.e2e.test.ts
+++ b/apps/cli/commands/tests/import.e2e.test.ts
@@ -17,6 +17,7 @@
  */
 import fs from 'fs';
 import path from 'path';
+import * as tar from 'tar';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
 import {
 	cleanupCliEnv,
@@ -187,4 +188,87 @@ describe.skipIf( ! cliE2ePrerequisitesMet() )( 'CLI e2e: studio import', () => {
 			expect( await getBlogname( env, sitePath ) ).toBe( FIXTURE_BLOGNAME );
 		}
 	);
+
+	// Regression test for https://github.com/Automattic/studio/issues/3518
+	// where db.php overwrites SQLite drop-in during restore causing database import error
+	// "Could not determine the version of the SQLite integration plugin".
+	it(
+		'imports a backup containing db.php drop-in',
+		{ tags: [ 'e2e' ], timeout: 300_000 },
+		async () => {
+			if ( ! env ) {
+				throw new Error( 'CLI e2e env was not initialised' );
+			}
+
+			const workDir = path.join( env.root, 'db-php' );
+			const cwd = path.join( workDir, 'contents' );
+			fs.mkdirSync( cwd, { recursive: true } );
+			await tar.x( { file: path.join( FIXTURES_DIR, 'jetpack-backup.tar.gz' ), cwd } );
+
+			fs.writeFileSync(
+				path.join( cwd, 'wp-content', 'db.php' ),
+				'<?php\n/**\n * Plugin Name: Query Monitor Database Class (Drop-in)\n */\nclass QM_DB extends wpdb {}\n'
+			);
+
+			const file = path.join( workDir, 'jetpack-backup-db-php-replaced.tar.gz' );
+			await tar.c( { file, cwd, gzip: true }, fs.readdirSync( cwd ) );
+			const sitePath = await createStoppedSite(
+				env,
+				'Foreign DB Import E2E Site',
+				'import-db-php'
+			);
+
+			const result = await runCli( [ 'import', file, '--path', sitePath ], env );
+			expect( result.code, result.stderr ).toBe( 0 );
+
+			const db = fs.readFileSync( path.join( sitePath, 'wp-content', 'db.php' ), 'utf8' );
+			expect( db ).toContain( 'SQLITE_DB_DROPIN_VERSION' );
+			expect( db ).not.toContain( 'QM_DB' );
+
+			assertImportedSiteOnDisk( sitePath );
+			expect( await getBlogname( env, sitePath ) ).toBe( FIXTURE_BLOGNAME );
+		}
+	);
+
+	it(
+		'rejects a database backup before mutating a site configured for MySQL',
+		{ tags: [ 'e2e' ], timeout: 300_000 },
+		async () => {
+			if ( ! env ) {
+				throw new Error( 'CLI e2e env was not initialised' );
+			}
+
+			const sitePath = await createStoppedSite( env, 'MySQL Import E2E Site', 'import-mysql' );
+			const sqlitePaths = [
+				path.join( sitePath, 'wp-content', 'db.php' ),
+				path.join( sitePath, 'wp-content', 'database', '.ht.sqlite' ),
+				path.join( sitePath, 'wp-content', 'mu-plugins', 'sqlite-database-integration' ),
+			];
+			fs.copyFileSync(
+				path.join( sitePath, 'wp-config-sample.php' ),
+				path.join( sitePath, 'wp-config.php' )
+			);
+
+			for ( const sqlitePath of sqlitePaths ) {
+				fs.rmSync( sqlitePath, { recursive: true, force: true } );
+			}
+			expect( fs.existsSync( path.join( sitePath, 'wp-config.php' ) ) ).toBe( true );
+
+			const result = await runCli(
+				[ 'import', path.join( FIXTURES_DIR, 'jetpack-backup.tar.gz' ), '--path', sitePath ],
+				env
+			);
+			expect( result.code ).not.toBe( 0 );
+			expect( result.stderr ).toContain(
+				'Database import requires SQLite, but this site is configured to use an external database.'
+			);
+
+			for ( const sqlitePath of sqlitePaths ) {
+				expect( fs.existsSync( sqlitePath ) ).toBe( false );
+			}
+			expect( fs.existsSync( path.join( sitePath, 'wp-content', 'themes', 'mypet-theme' ) ) ).toBe(
+				false
+			);
+		}
+	);
 } );
diff --git a/apps/cli/lib/import-export/import/importers/importer.ts b/apps/cli/lib/import-export/import/importers/importer.ts
index 16b8e2d94b..47f3758857 100644
--- a/apps/cli/lib/import-export/import/importers/importer.ts
+++ b/apps/cli/lib/import-export/import/importers/importer.ts
@@ -17,6 +17,7 @@ import semver from 'semver';
 import trash from 'trash';
 import { SiteData } from 'cli/lib/cli-config/core';
 import { runWpCliCommand } from 'cli/lib/run-wp-cli-command';
+import { installSqliteIntegration, needsSqliteSetup } from 'cli/lib/sqlite-integration';
 import { ImportExportEventEmitter } from '../../events';
 import { BackupContents, MetaFileData } from '../types';
 import { updateSiteUrl } from '../update-site-url';
@@ -66,17 +67,31 @@ abstract class BaseImporter extends ImportExportEventEmitter implements Importer
 
 	abstract import( site: SiteData ): Promise< ImporterResult >;
 
+	protected async assertSqliteDatabaseImportSupported( site: SiteData ): Promise< void > {
+		if ( ! ( await needsSqliteSetup( site.path ) ) ) {
+			throw new Error(
+				__(
+					'Database import requires SQLite, but this site is configured to use an external database.'
+				)
+			);
+		}
+	}
+
 	protected async importDatabase( site: SiteData, sqlFiles: string[] ): Promise< void > {
 		if ( ! sqlFiles.length ) {
 			return;
 		}
 
+		await this.assertSqliteDatabaseImportSupported( site );
 		this.emit( ImportEvents.IMPORT_DATABASE_START );
 
 		const sortedSqlFiles = sqlFiles.sort( ( a, b ) => a.localeCompare( b ) );
 		let processedFiles = 0;
 		const totalFiles = sortedSqlFiles.length;
 
+		// db.php may be non-SQLite drop-in from backup
+		await installSqliteIntegration( site.path );
+
 		for ( const sqlFile of sortedSqlFiles ) {
 			const sqlTempFile = `${ generateBackupFilename( 'sql' ) }.sql`;
 			const tmpPath = path.join( site.path, sqlTempFile );
@@ -145,6 +160,10 @@ abstract class BaseBackupImporter extends BaseImporter {
 
 	async import( site: SiteData ): Promise< ImporterResult > {
 		try {
+			if ( this.backup.sqlFiles.length ) {
+				// Classify the destination before restored files can make MySQL look like SQLite.
+				await this.assertSqliteDatabaseImportSupported( site );
+			}
 			if ( this.shouldCleanUpBeforeImport ) {
 				await this.moveExistingWpContentToTrash( site.path );
 			}
diff --git a/apps/cli/lib/sqlite-integration.ts b/apps/cli/lib/sqlite-integration.ts
index a5a5ee3151..a5e57a732d 100644
--- a/apps/cli/lib/sqlite-integration.ts
+++ b/apps/cli/lib/sqlite-integration.ts
@@ -24,6 +24,10 @@ export async function installSqliteIntegration( sitePath: string ) {
 	return provider.installSqliteIntegration( sitePath );
 }
 
+export async function needsSqliteSetup( sitePath: string ) {
+	return provider.needsSqliteSetup( sitePath );
+}
+
 export async function keepSqliteIntegrationUpdated( sitePath: string ) {
 	return provider.keepSqliteIntegrationUpdated( sitePath );
 }