diff --git a/src/init.ts b/src/init.ts
index a674cb19f..5968176fe 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -253,11 +253,14 @@ export async function installPythonDeps(codeql: CodeQL, logger: Logger) {
     if (process.platform === "win32") {
       await new toolrunner.ToolRunner(await safeWhich.safeWhich("py"), [
         "-3",
+        "-B",
         path.join(scriptsFolder, script),
         path.dirname(codeql.getPath()),
       ]).exec();
     } else {
-      await new toolrunner.ToolRunner(path.join(scriptsFolder, script), [
+      await new toolrunner.ToolRunner(await safeWhich.safeWhich("python3"), [
+        "-B",
+        path.join(scriptsFolder, script),
         path.dirname(codeql.getPath()),
       ]).exec();
     }