diff --git a/packages/babel-core/src/transformation/normalize-file.js b/packages/babel-core/src/transformation/normalize-file.js
index 203488acd6..38a015f1ac 100644
--- a/packages/babel-core/src/transformation/normalize-file.js
+++ b/packages/babel-core/src/transformation/normalize-file.js
@@ -2,6 +2,7 @@
 
 import path from "path";
 import buildDebug from "debug";
+import cloneDeep from "lodash/cloneDeep";
 import * as t from "@babel/types";
 import type { PluginPasses } from "../config";
 import convertSourceMap, { typeof Converter } from "convert-source-map";
@@ -75,6 +76,7 @@ export default function normalizeFile(
     } else if (ast.type !== "File") {
       throw new Error("AST root must be a Program or File node");
     }
+    ast = cloneDeep(ast);
   } else {
     // The parser's AST types aren't fully compatible with the types generated
     // by the logic in babel-types.
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index a3b4568a7a..5c3a97c7a3 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -12,6 +12,13 @@ function assertNotIgnored(result) {
   expect(result).not.toBeNull();
 }
 
+function parse(code, opts) {
+  return babel.parse(code, {
+    cwd: __dirname,
+    ...opts,
+  });
+}
+
 function transform(code, opts) {
   return babel.transform(code, {
     cwd: __dirname,
@@ -43,6 +50,13 @@ function transformAsync(code, opts) {
   });
 }
 
+function transformFromAst(ast, code, opts) {
+  return babel.transformFromAst(ast, code, {
+    cwd: __dirname,
+    ...opts,
+  });
+}
+
 describe("parser and generator options", function() {
   const recast = {
     parse: function(code, opts) {
@@ -168,6 +182,30 @@ describe("api", function() {
     expect(options).toEqual({ babelrc: false });
   });
 
+  it("transformFromAst should not mutate the AST", function() {
+    const program = "const identifier = 1";
+    const node = parse(program);
+    const { code } = transformFromAst(node, program, {
+      plugins: [
+        function() {
+          return {
+            visitor: {
+              Identifier: function(path) {
+                path.node.name = "replaced";
+              },
+            },
+          };
+        },
+      ],
+    });
+
+    expect(code).toBe("const replaced = 1;");
+    expect(node.program.body[0].declarations[0].id.name).toBe(
+      "identifier",
+      "original ast should not have been mutated",
+    );
+  });
+
   it("options throw on falsy true", function() {
     return expect(function() {
       transform("", {