diff --git a/index.js b/index.js
index f4b464c..2293e23 100644
--- a/index.js
+++ b/index.js
@@ -16,11 +16,15 @@ const {
  *   publishDir: string to path
  * }
  */
+
 const nextOnNetlify = (options = {}) => {
   const functionsPath = options.functionsDir || NETLIFY_FUNCTIONS_PATH;
   const publishPath = options.publishDir || NETLIFY_PUBLISH_PATH;
 
-  prepareFolders({ functionsPath, publishPath });
+  const trackNextOnNetlifyFiles = prepareFolders({
+    functionsPath,
+    publishPath,
+  });
 
   copyPublicFiles(publishPath);
 
@@ -33,6 +37,8 @@ const nextOnNetlify = (options = {}) => {
   setupRedirects(publishPath);
 
   setupHeaders(publishPath);
+
+  trackNextOnNetlifyFiles();
 };
 
 module.exports = nextOnNetlify;
diff --git a/lib/helpers/handleFileTracking.js b/lib/helpers/handleFileTracking.js
new file mode 100644
index 0000000..736d9f5
--- /dev/null
+++ b/lib/helpers/handleFileTracking.js
@@ -0,0 +1,80 @@
+const { join } = require("path");
+const {
+  existsSync,
+  readdirSync,
+  readFileSync,
+  writeFileSync,
+  removeSync,
+} = require("fs-extra");
+const findCacheDir = require("find-cache-dir");
+const { NETLIFY_PUBLISH_PATH, NETLIFY_FUNCTIONS_PATH } = require("../config");
+
+const TRACKING_FILE_SEPARATOR = "---";
+
+// Clean configured publish and functions folders and track next-on-netlify files
+// for future cleans
+const handleFileTracking = ({ functionsPath, publishPath }) => {
+  const isConfiguredFunctionsDir = functionsPath !== NETLIFY_FUNCTIONS_PATH;
+  const isConfiguredPublishDir = publishPath !== NETLIFY_PUBLISH_PATH;
+
+  const cacheDir = findCacheDir({ name: "next-on-netlify", create: true });
+  const trackingFilePath = join(cacheDir, ".nonfiletracking");
+
+  if (existsSync(trackingFilePath)) {
+    const trackingFile = readFileSync(trackingFilePath, "utf8");
+    const [trackedFunctions, trackedPublish] = trackingFile.split(
+      TRACKING_FILE_SEPARATOR
+    );
+
+    const cleanConfiguredFiles = (trackedFiles) => {
+      trackedFiles.forEach((file) => {
+        const filePath = join(publishPath, file);
+        if (file !== "" && existsSync(filePath)) {
+          removeSync(filePath);
+        }
+      });
+    };
+
+    if (isConfiguredPublishDir) {
+      cleanConfiguredFiles(trackedPublish.split("\n"));
+    }
+    if (isConfiguredFunctionsDir) {
+      cleanConfiguredFiles(trackedFunctions.split("\n"));
+    }
+  }
+
+  const functionsBeforeRun = existsSync(functionsPath)
+    ? readdirSync(functionsPath)
+    : [];
+  const publishBeforeRun = existsSync(publishPath)
+    ? readdirSync(publishPath)
+    : [];
+
+  // this callback will run at the end of nextOnNetlify()
+  const trackNewFiles = () => {
+    const functionsAfterRun = isConfiguredFunctionsDir
+      ? readdirSync(functionsPath)
+      : functionsBeforeRun;
+    const publishAfterRun = isConfiguredPublishDir
+      ? readdirSync(publishPath)
+      : publishBeforeRun;
+    const getDifference = (before, after) =>
+      after.filter((filePath) => !before.includes(filePath));
+    const newFunctionsFiles = getDifference(
+      functionsBeforeRun,
+      functionsAfterRun
+    );
+    const newPublishFiles = getDifference(publishBeforeRun, publishAfterRun);
+
+    const allTrackedFiles = [
+      ...newFunctionsFiles,
+      TRACKING_FILE_SEPARATOR,
+      ...newPublishFiles,
+    ];
+    writeFileSync(trackingFilePath, allTrackedFiles.join("\n"));
+  };
+
+  return trackNewFiles;
+};
+
+module.exports = handleFileTracking;
diff --git a/lib/steps/prepareFolders.js b/lib/steps/prepareFolders.js
index af497ac..cb65598 100644
--- a/lib/steps/prepareFolders.js
+++ b/lib/steps/prepareFolders.js
@@ -1,26 +1,37 @@
+const { join } = require("path");
 const { emptyDirSync } = require("fs-extra");
+const findCacheDir = require("find-cache-dir");
 const { logTitle, log } = require("../helpers/logger");
 const { NETLIFY_PUBLISH_PATH, NETLIFY_FUNCTIONS_PATH } = require("../config");
+const handleFileTracking = require("../helpers/handleFileTracking");
 
-// Empty existing publish and functions folders
+// Clean existing publish and functions folders
 const prepareFolders = ({ functionsPath, publishPath }) => {
   logTitle("🚀 Next on Netlify 🚀");
 
-  if (functionsPath === NETLIFY_FUNCTIONS_PATH) {
+  const isNotConfiguredFunctionsDir = functionsPath === NETLIFY_FUNCTIONS_PATH;
+  const isNotConfiguredPublishDir = publishPath === NETLIFY_PUBLISH_PATH;
+
+  if (isNotConfiguredFunctionsDir) {
     log("  ", "Functions directory: ", functionsPath);
   }
-  if (publishPath === NETLIFY_PUBLISH_PATH) {
+  if (isNotConfiguredPublishDir) {
     log("  ", "Publish directory: ", publishPath);
   }
-  if (
-    functionsPath === NETLIFY_FUNCTIONS_PATH ||
-    publishPath === NETLIFY_PUBLISH_PATH
-  ) {
+  if (isNotConfiguredFunctionsDir || isNotConfiguredPublishDir) {
     log("  ", "Make sure these are set in your netlify.toml file.");
   }
 
-  if (publishPath === NETLIFY_PUBLISH_PATH) emptyDirSync(publishPath);
-  if (functionsPath === NETLIFY_FUNCTIONS_PATH) emptyDirSync(functionsPath);
+  // We can empty these dirs knowing there will only be stale NoN-generated files inside
+  if (isNotConfiguredPublishDir) {
+    emptyDirSync(publishPath);
+  }
+  if (isNotConfiguredFunctionsDir) {
+    emptyDirSync(functionsPath);
+  }
+
+  // This returns a function that runs as the last step of nextOnNetlify()
+  return handleFileTracking({ functionsPath, publishPath });
 };
 
 module.exports = prepareFolders;
diff --git a/tests/configurableDirs.test.js b/tests/configurableDirs.test.js
new file mode 100644
index 0000000..aa122a7
--- /dev/null
+++ b/tests/configurableDirs.test.js
@@ -0,0 +1,147 @@
+// Test next-on-netlify when config is set from a function in next.config.js
+// See: https://github.com/netlify/next-on-netlify/issues/25
+
+const { parse, join } = require("path");
+const { existsSync, readdirSync, readFileSync } = require("fs-extra");
+const buildNextApp = require("./helpers/buildNextApp");
+
+// The name of this test file (without extension)
+const FILENAME = parse(__filename).name;
+
+// The directory which will be used for testing.
+// We simulate a NextJS app within that directory, with pages, and a
+// package.json file.
+const PROJECT_PATH = join(__dirname, "builds", FILENAME);
+const FUNCTIONS_DIR = "my-functions";
+const PUBLISH_DIR = "my-publish";
+
+// Capture the output to verify successful build
+let buildOutput;
+
+beforeAll(
+  async () => {
+    runOutput = await buildNextApp()
+      .forTest(__filename)
+      .withPages("pages")
+      .withNextConfig("next.config.js")
+      .withPackageJson("package.json")
+      .withCustomFunctions("my-functions")
+      .runWithRequire({ functionsDir: FUNCTIONS_DIR, publishDir: PUBLISH_DIR });
+  },
+  // time out after 180 seconds
+  180 * 1000
+);
+
+describe("next-on-netlify", () => {
+  const functionsDir = join(PROJECT_PATH, FUNCTIONS_DIR);
+
+  test("builds successfully", () => {
+    expect(runOutput).toMatch("Built successfully!");
+  });
+
+  test("copies custom Netlify Function to configured functions directory", () => {
+    expect(existsSync(join(functionsDir, "someTestFunction.js"))).toBe(true);
+  });
+
+  test("creates a Netlify Function for each SSR page", () => {
+    expect(existsSync(join(functionsDir, "next_index", "next_index.js"))).toBe(
+      true
+    );
+    expect(
+      existsSync(join(functionsDir, "next_shows_id", "next_shows_id.js"))
+    ).toBe(true);
+    expect(
+      existsSync(
+        join(functionsDir, "next_shows_params", "next_shows_params.js")
+      )
+    ).toBe(true);
+    expect(
+      existsSync(
+        join(
+          functionsDir,
+          "next_getServerSideProps_static",
+          "next_getServerSideProps_static.js"
+        )
+      )
+    ).toBe(true);
+    expect(
+      existsSync(
+        join(
+          functionsDir,
+          "next_getServerSideProps_id",
+          "next_getServerSideProps_id.js"
+        )
+      )
+    ).toBe(true);
+  });
+
+  test("copies static pages to output directory", () => {
+    const OUTPUT_PATH = join(PROJECT_PATH, PUBLISH_DIR);
+
+    expect(existsSync(join(OUTPUT_PATH, "static.html"))).toBe(true);
+    expect(existsSync(join(OUTPUT_PATH, "static/[id].html"))).toBe(true);
+  });
+
+  test("copies static assets to out_publish/_next/ directory", () => {
+    const dirs = readdirSync(
+      join(PROJECT_PATH, PUBLISH_DIR, "_next", "static")
+    );
+
+    expect(dirs.length).toBe(2);
+    expect(dirs).toContain("chunks");
+  });
+});
+
+describe("clean up of NoN files", () => {
+  test("creates a .nonfiletracking to audit NoN-specific files between builds", () => {
+    const cacheDir = join(PROJECT_PATH, "/node_modules/.cache/next-on-netlify");
+    const dirs = readdirSync(cacheDir);
+    expect(dirs[0]).toEqual(".nonfiletracking");
+  });
+
+  test(".nonfiletracking contains NoN-specific files", () => {
+    const cacheDir = join(PROJECT_PATH, "/node_modules/.cache/next-on-netlify");
+    const fileList = readFileSync(join(cacheDir, ".nonfiletracking"), "utf8");
+    // had to test equality this way because of windows :)
+    const isSameList = (arr1, arr2) =>
+      arr1.reduce((isSame, func) => {
+        if (arr2.includes(func)) {
+          isSame = true;
+        } else {
+          isSame = false;
+        }
+        return isSame;
+      }, true);
+    const nextFunctions = [
+      "next_api_shows_id",
+      "next_api_shows_params",
+      "next_api_static",
+      "next_getServerSideProps_all_slug",
+      "next_getServerSideProps_id",
+      "next_getServerSideProps_static",
+      "next_getStaticProps_id",
+      "next_getStaticProps_static",
+      "next_getStaticProps_withFallback_id",
+      "next_getStaticProps_withFallback_slug",
+      "next_getStaticProps_withRevalidate_id",
+      "next_getStaticProps_withRevalidate_withFallback_id",
+      "next_getStaticProps_withrevalidate",
+      "next_index",
+      "next_shows_id",
+      "next_shows_params",
+    ];
+    const fileListFunctions = fileList.split("---")[0].split("\n");
+    expect(isSameList(nextFunctions, fileListFunctions)).toBe(true);
+    expect(fileListFunctions.includes("someTestFunction.js")).toBe(false);
+    const publishFiles = [
+      "404.html",
+      "_next",
+      "_redirects",
+      "getStaticProps",
+      "static",
+      "static.html",
+    ];
+    const fileListPublish = fileList.split("---")[1].split("\n");
+    expect(isSameList(publishFiles, fileListPublish)).toBe(true);
+  });
+});
diff --git a/tests/fixtures/my-functions/someTestFunction.js b/tests/fixtures/my-functions/someTestFunction.js
new file mode 100644
index 0000000..e69de29
diff --git a/tests/helpers/buildNextApp.js b/tests/helpers/buildNextApp.js
index eaee609..8073da6 100644
--- a/tests/helpers/buildNextApp.js
+++ b/tests/helpers/buildNextApp.js
@@ -46,6 +46,10 @@ class NextAppBuilder {
     return this.withFile(packageJsonFile, "package.json");
   }
 
+  withCustomFunctions(functionsDir) {
+    return this.withFile(functionsDir);
+  }
+
   // Copy a file from the fixtures folder to the app's staging folder
   withFile(fixture, target = null) {
     // If no target file name is given, use the same name as the fixture
@@ -61,9 +65,8 @@ class NextAppBuilder {
     return this;
   }
 
-  // Build the application with next build
-  async build() {
-    // Generate a cach hash ID from the current contents of the staging folder.
+  async buildNextApp() {
+    // Generate a cache hash ID from the current contents of the staging folder.
     const { hash: cacheHash } = await hashElement(this.__stagingPath, {
       encoding: "hex",
     });
@@ -83,11 +86,29 @@ class NextAppBuilder {
     // run next-on-netlify
     copySync(this.__cachePath, this.__appPath);
 
-    // Run next-on-netlify
+    process.chdir(this.__appPath);
+  }
+
+  async build() {
+    await this.buildNextApp();
+
+    // Run next-on-netlify as postbuild script
     const { stdout } = await npmRun("next-on-netlify", this.__appPath);
     return stdout;
   }
 
+  async runWithRequire(options) {
+    await this.buildNextApp();
+
+    // Run next-on-netlify as an imported module
+    const nextOnNetlify = require("../..");
+    nextOnNetlify({
+      functionsDir: join(this.__appPath, options.functionsDir),
+      publishDir: join(this.__appPath, options.publishDir),
+    });
+    return "Built successfully!";
+  }
+
   /*****************************************************************************
    * Private functions
    ****************************************************************************/