diff --git a/node/formats/javascript.ts b/node/formats/javascript.ts
index 8b0ce265..0e7ae209 100644
--- a/node/formats/javascript.ts
+++ b/node/formats/javascript.ts
@@ -1,4 +1,4 @@
-import { mkdir, rm, writeFile } from 'fs/promises'
+import { mkdir, writeFile } from 'fs/promises'
 import { join } from 'path'
 import { pathToFileURL } from 'url'
 
@@ -27,7 +27,6 @@ const generateStage2 = async ({
   formatImportError,
   functions,
 }: GenerateStage2Options) => {
-  await rm(distDirectory, { force: true, recursive: true, maxRetries: 3 })
   await mkdir(distDirectory, { recursive: true })
 
   const entryPoint = getLocalEntryPoint(functions, { bootstrapURL, formatExportTypeError, formatImportError })
diff --git a/node/npm_dependencies.ts b/node/npm_dependencies.ts
index ec204e8d..419b3389 100644
--- a/node/npm_dependencies.ts
+++ b/node/npm_dependencies.ts
@@ -326,5 +326,6 @@ export const vendorNPMSpecifiers = async ({
     directory: temporaryDirectory.path,
     importMap: newImportMap,
     npmSpecifiersWithExtraneousFiles,
+    outputFiles: outputFiles.map((file) => file.path),
   }
 }
diff --git a/node/server/server.ts b/node/server/server.ts
index ff060679..b036037f 100644
--- a/node/server/server.ts
+++ b/node/server/server.ts
@@ -1,3 +1,6 @@
+import { readdir, unlink } from 'fs/promises'
+import { join } from 'path'
+
 import { DenoBridge, OnAfterDownloadHook, OnBeforeDownloadHook, ProcessRef } from '../bridge.js'
 import { getFunctionConfig, FunctionConfig } from '../config.js'
 import type { EdgeFunction } from '../edge_function.js'
@@ -32,6 +35,17 @@ interface StartServerOptions {
   getFunctionsConfig?: boolean
 }
 
+/**
+ * Cleans up a directory, except for the files specified in the `except` array.
+ * Both should be given as absolute paths.
+ * Assumes the directory doesn't contain any nested directories.
+ */
+const cleanDirectory = async (directory: string, except: string[]) => {
+  const files = await readdir(directory)
+  const toBeDeleted = files.filter((file) => !except.includes(join(directory, file)))
+  await Promise.all(toBeDeleted.map((file) => unlink(join(directory, file))))
+}
+
 const prepareServer = ({
   basePath,
   bootstrapURL,
@@ -70,6 +84,9 @@ const prepareServer = ({
     const importMap = baseImportMap.clone()
     const npmSpecifiersWithExtraneousFiles: string[] = []
 
+    // we keep track of the files that are relevant to the user's code, so we can clean up leftovers from past executions later
+    const relevantFiles = [stage2Path]
+
     const vendor = await vendorNPMSpecifiers({
       basePath,
       directory: distDirectory,
@@ -83,8 +100,11 @@ const prepareServer = ({
       features.npmModules = true
       importMap.add(vendor.importMap)
       npmSpecifiersWithExtraneousFiles.push(...vendor.npmSpecifiersWithExtraneousFiles)
+      relevantFiles.push(...vendor.outputFiles)
     }
 
+    await cleanDirectory(distDirectory, relevantFiles)
+
     try {
       // This command will print a JSON object with all the modules found in
       // the `stage2Path` file as well as all of their dependencies.