diff --git a/src/hooks/tests/use-chat-context.test.tsx b/src/hooks/tests/use-chat-context.test.tsx
index e41ebaa7c..3efe1f619 100644
--- a/src/hooks/tests/use-chat-context.test.tsx
+++ b/src/hooks/tests/use-chat-context.test.tsx
@@ -123,10 +123,12 @@ describe( 'useChatContext hook', () => {
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 1, {
 				siteId: SELECTED_SITE.id,
 				args: 'plugin list --format=json --status=active',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 2, {
 				siteId: SELECTED_SITE.id,
 				args: 'theme list --format=json',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenCalledTimes( 2 );
 		} );
@@ -234,10 +236,12 @@ describe( 'useChatContext hook', () => {
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 1, {
 				siteId: ANOTHER_SITE.id,
 				args: 'plugin list --format=json --status=active',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 2, {
 				siteId: ANOTHER_SITE.id,
 				args: 'theme list --format=json',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenCalledTimes( 2 );
 		} );
@@ -288,10 +292,12 @@ describe( 'useChatContext hook', () => {
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 1, {
 				siteId: SELECTED_SITE.id,
 				args: 'plugin list --format=json --status=active',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 2, {
 				siteId: SELECTED_SITE.id,
 				args: 'theme list --format=json',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenCalledTimes( 2 );
 		} );
@@ -391,10 +397,12 @@ describe( 'useChatContext hook', () => {
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 1, {
 				siteId: NEW_SITE.id,
 				args: 'plugin list --format=json --status=active',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 2, {
 				siteId: NEW_SITE.id,
 				args: 'theme list --format=json',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenCalledTimes( 2 );
 		} );
@@ -436,10 +444,12 @@ describe( 'useChatContext hook', () => {
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 1, {
 				siteId: SELECTED_SITE.id,
 				args: 'plugin list --format=json --status=active',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenNthCalledWith( 2, {
 				siteId: SELECTED_SITE.id,
 				args: 'theme list --format=json',
+				skipPluginsAndThemes: true,
 			} );
 			expect( getIpcApi().executeWPCLiInline ).toHaveBeenCalledTimes( 2 );
 		} );
diff --git a/src/hooks/use-chat-context.tsx b/src/hooks/use-chat-context.tsx
index fbca2cc9d..ce502e9e8 100644
--- a/src/hooks/use-chat-context.tsx
+++ b/src/hooks/use-chat-context.tsx
@@ -80,6 +80,7 @@ export const ChatProvider: React.FC< ChatProviderProps > = ( { children } ) => {
 		const { stdout, stderr } = await getIpcApi().executeWPCLiInline( {
 			siteId,
 			args: 'plugin list --format=json --status=active',
+			skipPluginsAndThemes: true,
 		} );
 		if ( stderr ) {
 			return [];
@@ -91,6 +92,7 @@ export const ChatProvider: React.FC< ChatProviderProps > = ( { children } ) => {
 		const { stdout, stderr } = await getIpcApi().executeWPCLiInline( {
 			siteId,
 			args: 'theme list --format=json',
+			skipPluginsAndThemes: true,
 		} );
 		if ( stderr ) {
 			return [];
diff --git a/src/hooks/use-execute-cli.ts b/src/hooks/use-execute-cli.ts
index fc8920f3a..702129102 100644
--- a/src/hooks/use-execute-cli.ts
+++ b/src/hooks/use-execute-cli.ts
@@ -28,6 +28,7 @@ export function useExecuteWPCLI(
 		const result = await getIpcApi().executeWPCLiInline( {
 			siteId: siteId || '',
 			args: args.join( ' ' ),
+			skipPluginsAndThemes: false,
 		} );
 
 		const msTime = Date.now() - startTime;
diff --git a/src/ipc-handlers.ts b/src/ipc-handlers.ts
index 2409d9863..8e47b47a7 100644
--- a/src/ipc-handlers.ts
+++ b/src/ipc-handlers.ts
@@ -815,7 +815,15 @@ export async function saveOnboarding(
 
 export async function executeWPCLiInline(
 	_event: IpcMainInvokeEvent,
-	{ siteId, args }: { siteId: string; args: string }
+	{
+		siteId,
+		args,
+		skipPluginsAndThemes = false,
+	}: {
+		siteId: string;
+		args: string;
+		skipPluginsAndThemes?: boolean;
+	}
 ): Promise< WpCliResult > {
 	if ( SiteServer.isDeleted( siteId ) ) {
 		return {
@@ -828,7 +836,9 @@ export async function executeWPCLiInline(
 	if ( ! server ) {
 		throw new Error( 'Site not found.' );
 	}
-	return server.executeWpCliCommand( args );
+	return server.executeWpCliCommand( args, {
+		skipPluginsAndThemes,
+	} );
 }
 
 export async function getThumbnailData( _event: IpcMainInvokeEvent, id: string ) {
diff --git a/src/lib/import-export/export/export-database.ts b/src/lib/import-export/export/export-database.ts
index ddea88d33..3667f9b52 100644
--- a/src/lib/import-export/export/export-database.ts
+++ b/src/lib/import-export/export/export-database.ts
@@ -18,7 +18,10 @@ export async function exportDatabaseToFile(
 
 	// Execute the command to export directly to the temp file
 	const { stderr, exitCode } = await server.executeWpCliCommand(
-		`sqlite export ${ tempFileName } --require=/tmp/sqlite-command/command.php`
+		`sqlite export ${ tempFileName } --require=/tmp/sqlite-command/command.php`,
+		{
+			skipPluginsAndThemes: true,
+		}
 	);
 
 	if ( stderr ) {
@@ -47,7 +50,10 @@ export async function exportDatabaseToMultipleFiles(
 	}
 
 	const tablesResult = await server.executeWpCliCommand(
-		`sqlite tables --format=json --require=/tmp/sqlite-command/command.php`
+		`sqlite tables --format=json --require=/tmp/sqlite-command/command.php`,
+		{
+			skipPluginsAndThemes: true,
+		}
 	);
 	if ( tablesResult.stderr ) {
 		throw new Error( `Database export failed: ${ tablesResult.stderr }` );
@@ -79,7 +85,10 @@ export async function exportDatabaseToMultipleFiles(
 
 		// Execute the command to export directly to a temporary file in the project directory
 		const { stderr, exitCode } = await server.executeWpCliCommand(
-			`sqlite export ${ fileName } --tables=${ table } --require=/tmp/sqlite-command/command.php`
+			`sqlite export ${ fileName } --tables=${ table } --require=/tmp/sqlite-command/command.php`,
+			{
+				skipPluginsAndThemes: true,
+			}
 		);
 
 		if ( stderr ) {
diff --git a/src/lib/import-export/export/exporters/default-exporter.ts b/src/lib/import-export/export/exporters/default-exporter.ts
index 6e3eff2c2..eb436c0e9 100644
--- a/src/lib/import-export/export/exporters/default-exporter.ts
+++ b/src/lib/import-export/export/exporters/default-exporter.ts
@@ -268,7 +268,10 @@ export class DefaultExporter extends EventEmitter implements Exporter {
 		}
 
 		const { stderr, stdout } = await server.executeWpCliCommand(
-			'plugin list --status=active,inactive --fields=name,status,version --format=json'
+			'plugin list --status=active,inactive --fields=name,status,version --format=json',
+			{
+				skipPluginsAndThemes: true,
+			}
 		);
 
 		if ( stderr ) {
@@ -296,7 +299,10 @@ export class DefaultExporter extends EventEmitter implements Exporter {
 		}
 
 		const { stderr, stdout } = await server.executeWpCliCommand(
-			'theme list --fields=name,status,version --format=json'
+			'theme list --fields=name,status,version --format=json',
+			{
+				skipPluginsAndThemes: true,
+			}
 		);
 
 		if ( stderr ) {
diff --git a/src/lib/import-export/import/importers/importer.ts b/src/lib/import-export/import/importers/importer.ts
index 4a61d9e80..3e3e7af33 100644
--- a/src/lib/import-export/import/importers/importer.ts
+++ b/src/lib/import-export/import/importers/importer.ts
@@ -57,7 +57,7 @@ abstract class BaseImporter extends EventEmitter implements Importer {
 				const { stderr, exitCode } = await server.executeWpCliCommand(
 					`sqlite import ${ sqlTempFile } --require=/tmp/sqlite-command/command.php`,
 					// SQLite plugin requires PHP 8+
-					{ targetPhpVersion: DEFAULT_PHP_VERSION }
+					{ targetPhpVersion: DEFAULT_PHP_VERSION, skipPluginsAndThemes: true }
 				);
 
 				if ( stderr ) {
@@ -86,7 +86,9 @@ abstract class BaseImporter extends EventEmitter implements Importer {
 			throw new Error( 'Site not found.' );
 		}
 
-		const { stdout: currentSiteUrl } = await server.executeWpCliCommand( `option get siteurl` );
+		const { stdout: currentSiteUrl } = await server.executeWpCliCommand( `option get siteurl`, {
+			skipPluginsAndThemes: true,
+		} );
 
 		if ( ! currentSiteUrl ) {
 			console.error( 'Failed to fetch site URL after import' );
@@ -96,7 +98,10 @@ abstract class BaseImporter extends EventEmitter implements Importer {
 		const studioUrl = `http://localhost:${ server.details.port }`;
 
 		const { stderr, exitCode } = await server.executeWpCliCommand(
-			`search-replace '${ currentSiteUrl.trim() }' '${ studioUrl.trim() }'`
+			`search-replace '${ currentSiteUrl.trim() }' '${ studioUrl.trim() }'`,
+			{
+				skipPluginsAndThemes: true,
+			}
 		);
 
 		if ( stderr ) {
diff --git a/src/lib/import-export/tests/export/exporters/sql-exporter.test.ts b/src/lib/import-export/tests/export/exporters/sql-exporter.test.ts
index 067a2e017..2dbd8e7ba 100644
--- a/src/lib/import-export/tests/export/exporters/sql-exporter.test.ts
+++ b/src/lib/import-export/tests/export/exporters/sql-exporter.test.ts
@@ -58,7 +58,10 @@ describe( 'SqlExporter', () => {
 
 		const siteServer = SiteServer.get( '123' );
 		expect( siteServer?.executeWpCliCommand ).toHaveBeenCalledWith(
-			'sqlite export studio-backup-db-export-2024-08-01-12-00-00.sql --require=/tmp/sqlite-command/command.php'
+			'sqlite export studio-backup-db-export-2024-08-01-12-00-00.sql --require=/tmp/sqlite-command/command.php',
+			{
+				skipPluginsAndThemes: true,
+			}
 		);
 	} );
 
diff --git a/src/lib/import-export/tests/import/importer/default-importer.test.ts b/src/lib/import-export/tests/import/importer/default-importer.test.ts
index fc4f3514c..416cc5edc 100644
--- a/src/lib/import-export/tests/import/importer/default-importer.test.ts
+++ b/src/lib/import-export/tests/import/importer/default-importer.test.ts
@@ -80,9 +80,11 @@ describe( 'JetpackImporter', () => {
 				'sqlite import studio-backup-sql-2024-08-01-12-00-00.sql --require=/tmp/sqlite-command/command.php';
 			expect( siteServer?.executeWpCliCommand ).toHaveBeenNthCalledWith( 1, expectedCommand, {
 				targetPhpVersion: '8.1',
+				skipPluginsAndThemes: true,
 			} );
 			expect( siteServer?.executeWpCliCommand ).toHaveBeenNthCalledWith( 2, expectedCommand, {
 				targetPhpVersion: '8.1',
+				skipPluginsAndThemes: true,
 			} );
 
 			const expectedUnlinkPath = '/path/to/studio/site/studio-backup-sql-2024-08-01-12-00-00.sql';
diff --git a/src/lib/import-export/tests/import/importer/playground-importer.test.ts b/src/lib/import-export/tests/import/importer/playground-importer.test.ts
index ab7defd03..82a1a4a3e 100644
--- a/src/lib/import-export/tests/import/importer/playground-importer.test.ts
+++ b/src/lib/import-export/tests/import/importer/playground-importer.test.ts
@@ -75,7 +75,9 @@ describe( 'localImporter', () => {
 			const siteServer = SiteServer.get( mockStudioSiteId );
 
 			const expectedCommand = 'option get siteurl';
-			expect( siteServer?.executeWpCliCommand ).toHaveBeenNthCalledWith( 1, expectedCommand );
+			expect( siteServer?.executeWpCliCommand ).toHaveBeenNthCalledWith( 1, expectedCommand, {
+				skipPluginsAndThemes: true,
+			} );
 
 			expect( move ).toHaveBeenNthCalledWith(
 				1,
diff --git a/src/site-server.ts b/src/site-server.ts
index 0784d3db6..102b650e8 100644
--- a/src/site-server.ts
+++ b/src/site-server.ts
@@ -168,7 +168,13 @@ export class SiteServer {
 
 	async executeWpCliCommand(
 		args: string,
-		{ targetPhpVersion }: { targetPhpVersion?: string } = {}
+		{
+			targetPhpVersion,
+			skipPluginsAndThemes = false,
+		}: {
+			targetPhpVersion?: string;
+			skipPluginsAndThemes?: boolean;
+		} = {}
 	): Promise< WpCliResult > {
 		const projectPath = this.details.path;
 		const phpVersion = targetPhpVersion ?? this.details.phpVersion;
@@ -180,6 +186,11 @@ export class SiteServer {
 
 		const wpCliArgs = parse( args );
 
+		if ( skipPluginsAndThemes ) {
+			wpCliArgs.push( '--skip-plugins' );
+			wpCliArgs.push( '--skip-themes' );
+		}
+
 		// The parsing of arguments can include shell operators like `>` or `||` that the app don't support.
 		const isValidCommand = wpCliArgs.every(
 			( arg: unknown ) => typeof arg === 'string' || arg instanceof String