diff --git a/lib/steps/prepareFolders.js b/lib/steps/prepareFolders.js
index 4cd75ce..e2dbd22 100644
--- a/lib/steps/prepareFolders.js
+++ b/lib/steps/prepareFolders.js
@@ -1,5 +1,6 @@
 const { emptyDirSync } = require("fs-extra");
 const { logTitle, log } = require("../helpers/logger");
+const { NETLIFY_PUBLISH_PATH, NETLIFY_FUNCTIONS_PATH } = require("../config");
 
 // Empty existing publish and functions folders
 const prepareFolders = ({ functionsPath, publishPath }) => {
@@ -8,8 +9,8 @@ const prepareFolders = ({ functionsPath, publishPath }) => {
   log("  ", "Publish directory: ", publishPath);
   log("  ", "Make sure these are set in your netlify.toml file.");
 
-  emptyDirSync(publishPath);
-  emptyDirSync(functionsPath);
+  if (publishPath === NETLIFY_PUBLISH_PATH) emptyDirSync(publishPath);
+  if (functionsPath === NETLIFY_FUNCTIONS_PATH) emptyDirSync(functionsPath);
 };
 
 module.exports = prepareFolders;