diff --git a/packages/babel-core/src/transformation/file/index.js b/packages/babel-core/src/transformation/file/index.js
index dad9ec5b13..f11e750303 100644
--- a/packages/babel-core/src/transformation/file/index.js
+++ b/packages/babel-core/src/transformation/file/index.js
@@ -45,7 +45,17 @@ export default class File extends Store {
     super();
 
     this.log = new Logger(this, opts.filename || "unknown");
-    this.opts = this.initOptions(opts);
+
+    opts = this.initOptions(opts);
+
+    let passes = [];
+    if (opts.plugins) passes.push(opts.plugins);
+
+    // With "passPerPreset" enabled there may still be presets in the options.
+    if (opts.presets) passes = passes.concat(opts.presets.map((preset) => preset.plugins).filter(Boolean));
+
+    this.pluginPasses = passes;
+    this.opts = opts;
 
     this.parserOpts = {
       sourceType: this.opts.sourceType,
@@ -53,22 +63,12 @@ export default class File extends Store {
       plugins: [],
     };
 
-    this.pluginVisitors = [];
-    this.pluginPasses = [];
-
-    // Plugins for top-level options.
-    this.buildPluginsForOptions(this.opts);
-
-    // If we are in the "pass per preset" mode, build
-    // also plugins for each preset.
-    if (this.opts.passPerPreset) {
-      // All the "per preset" options are inherited from the main options.
-      this.perPresetOpts = [];
-      this.opts.presets.forEach((presetOpts) => {
-        const perPresetOpts = Object.assign(Object.create(this.opts), presetOpts);
-        this.perPresetOpts.push(perPresetOpts);
-        this.buildPluginsForOptions(perPresetOpts);
-      });
+    for (const pluginPairs of passes) {
+      for (const [ plugin ] of pluginPairs) {
+        if (plugin.manipulateOptions) {
+          plugin.manipulateOptions(opts, this.parserOpts, this);
+        }
+      }
     }
 
     this.metadata = {
@@ -100,8 +100,7 @@ export default class File extends Store {
 
   static helpers: Array<string>;
 
-  pluginVisitors: Array<Object>;
-  pluginPasses: Array<PluginPass>;
+  pluginPasses: Array<Array<[Plugin, Object]>>;
   parserOpts: BabelParserOptions;
   log: Logger;
   opts: Object;
@@ -132,7 +131,7 @@ export default class File extends Store {
   }
 
   initOptions(opts) {
-    opts = new OptionManager(this.log).init(opts);
+    opts = this.log.wrap(() => new OptionManager().init(opts));
 
     if (opts.inputSourceMap) {
       opts.sourceMaps = true;
@@ -170,31 +169,6 @@ export default class File extends Store {
     return opts;
   }
 
-  buildPluginsForOptions(opts) {
-    if (!Array.isArray(opts.plugins)) {
-      return;
-    }
-
-    const plugins: Array<[PluginPass, Object]> = opts.plugins.concat(INTERNAL_PLUGINS);
-    const currentPluginVisitors = [];
-    const currentPluginPasses = [];
-
-    // init plugins!
-    for (const ref of plugins) {
-      const [plugin, pluginOpts] = ref; // todo: fix - can't embed in loop head because of flow bug
-
-      currentPluginVisitors.push(plugin.visitor);
-      currentPluginPasses.push(new PluginPass(this, plugin, pluginOpts));
-
-      if (plugin.manipulateOptions) {
-        plugin.manipulateOptions(opts, this.parserOpts, this);
-      }
-    }
-
-    this.pluginVisitors.push(currentPluginVisitors);
-    this.pluginPasses.push(currentPluginPasses);
-  }
-
   getModuleName(): ?string {
     const opts = this.opts;
     if (!opts.moduleIds) {
@@ -460,20 +434,25 @@ export default class File extends Store {
   }
 
   transform(): BabelFileResult {
-    // In the "pass per preset" mode, we have grouped passes.
-    // Otherwise, there is only one plain pluginPasses array.
-    for (let i = 0; i < this.pluginPasses.length; i++) {
-      const pluginPasses = this.pluginPasses[i];
-      this.call("pre", pluginPasses);
+    for (const pluginPairs of this.pluginPasses) {
+      const passes = [];
+      const visitors = [];
+
+      for (const [ plugin, pluginOpts ] of pluginPairs.concat(INTERNAL_PLUGINS)) {
+        const pass = new PluginPass(this, plugin, pluginOpts);
+        passes.push(pass);
+        visitors.push(plugin.visitor);
+      }
+
+      this.call("pre", passes);
       this.log.debug("Start transform traverse");
 
       // merge all plugin visitors into a single visitor
-      const visitor = traverse.visitors.merge(this.pluginVisitors[i], pluginPasses,
-        this.opts.wrapPluginVisitorMethod);
+      const visitor = traverse.visitors.merge(visitors, passes, this.opts.wrapPluginVisitorMethod);
       traverse(this.ast, visitor, this.scope);
 
       this.log.debug("End transform traverse");
-      this.call("post", pluginPasses);
+      this.call("post", passes);
     }
 
     return this.generate();
diff --git a/packages/babel-core/src/transformation/file/logger.js b/packages/babel-core/src/transformation/file/logger.js
index aa4a57d718..c07273e114 100644
--- a/packages/babel-core/src/transformation/file/logger.js
+++ b/packages/babel-core/src/transformation/file/logger.js
@@ -21,6 +21,15 @@ export default class Logger {
     return parts;
   }
 
+  wrap<T>(callback: () => T): T {
+    try {
+      return callback();
+    } catch (e) {
+      e.message = this._buildMessage(e.message);
+      throw e;
+    }
+  }
+
   warn(msg: string) {
     console.warn(this._buildMessage(msg));
   }
diff --git a/packages/babel-core/src/transformation/file/options/build-config-chain.js b/packages/babel-core/src/transformation/file/options/build-config-chain.js
index 5902d4c16e..a5af4e82ba 100644
--- a/packages/babel-core/src/transformation/file/options/build-config-chain.js
+++ b/packages/babel-core/src/transformation/file/options/build-config-chain.js
@@ -1,4 +1,3 @@
-import type Logger from "../logger";
 import resolve from "../../../helpers/resolve";
 import json5 from "json5";
 import path from "path";
@@ -21,9 +20,9 @@ function exists(filename) {
   }
 }
 
-export default function buildConfigChain(opts: Object = {}, log?: Logger) {
+export default function buildConfigChain(opts: Object = {}) {
   const filename = opts.filename;
-  const builder = new ConfigChainBuilder(log);
+  const builder = new ConfigChainBuilder();
 
   // resolve all .babelrc files
   if (opts.babelrc !== false) {
@@ -40,10 +39,9 @@ export default function buildConfigChain(opts: Object = {}, log?: Logger) {
 }
 
 class ConfigChainBuilder {
-  constructor(log?: Logger) {
+  constructor() {
     this.resolvedConfigs = [];
     this.configs = [];
-    this.log = log;
   }
 
   errorMultipleConfigs(loc1: string, loc2: string) {
@@ -183,7 +181,7 @@ class ConfigChainBuilder {
       if (extendsLoc) {
         this.addConfig(extendsLoc);
       } else {
-        if (this.log) this.log.error(`Couldn't resolve extends clause of ${options.extends} in ${alias}`);
+        throw new Error(`Couldn't resolve extends clause of ${options.extends} in ${alias}`);
       }
       delete options.extends;
     }
diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/transformation/file/options/option-manager.js
index 6c63ba32fa..762a643784 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/transformation/file/options/option-manager.js
@@ -1,5 +1,4 @@
 import * as context from "../../../index";
-import type Logger from "../logger";
 import Plugin from "../../plugin";
 import * as messages from "babel-messages";
 import { normaliseOptions } from "./index";
@@ -35,15 +34,13 @@ type MergeOptions = {
 };
 
 export default class OptionManager {
-  constructor(log?: Logger) {
+  constructor() {
     this.resolvedConfigs = [];
     this.options = OptionManager.createBareOptions();
-    this.log = log;
   }
 
   resolvedConfigs: Array<string>;
   options: Object;
-  log: ?Logger;
 
   static memoisedPlugins: Array<{
     container: Function;
@@ -158,7 +155,7 @@ export default class OptionManager {
 
     //
     if (typeof rawOpts !== "object" || Array.isArray(rawOpts)) {
-      this.log.error(`Invalid options type for ${alias}`, TypeError);
+      throw new TypeError(`Invalid options type for ${alias}`);
     }
 
     //
@@ -176,15 +173,14 @@ export default class OptionManager {
       const option = config[key];
 
       // check for an unknown option
-      if (!option && this.log) {
+      if (!option) {
         if (removed[key]) {
-          this.log.error(`Using removed Babel 5 option: ${alias}.${key} - ${removed[key].message}`,
-            ReferenceError);
+          throw new ReferenceError(`Using removed Babel 5 option: ${alias}.${key} - ${removed[key].message}`);
         } else {
           // eslint-disable-next-line max-len
           const unknownOptErr = `Unknown option: ${alias}.${key}. Check out http://babeljs.io/docs/usage/options/ for more information about options.`;
 
-          this.log.error(unknownOptErr, ReferenceError);
+          throw new ReferenceError(unknownOptErr);
         }
       }
     }
@@ -333,7 +329,7 @@ export default class OptionManager {
   }
 
   init(opts: Object = {}): Object {
-    for (const config of buildConfigChain(opts, this.log)) {
+    for (const config of buildConfigChain(opts)) {
       this.mergeOptions(config);
     }
 
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index bf03ff2f46..097b515b1a 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -141,7 +141,7 @@ describe("api", function () {
           plugins: [__dirname + "/../../babel-plugin-syntax-jsx", false],
         });
       },
-      /TypeError: Falsy value found in plugins/
+      /TypeError: \[BABEL\] unknown: Falsy value found in plugins/
     );
   });
 
diff --git a/packages/babel-core/test/option-manager.js b/packages/babel-core/test/option-manager.js
index a38436d197..126ed83c27 100644
--- a/packages/babel-core/test/option-manager.js
+++ b/packages/babel-core/test/option-manager.js
@@ -1,6 +1,5 @@
 import assert from "assert";
 import OptionManager from "../lib/transformation/file/options/option-manager";
-import Logger from "../lib/transformation/file/logger";
 import path from "path";
 
 describe("option-manager", () => {
@@ -17,7 +16,7 @@ describe("option-manager", () => {
     it("throws for removed babel 5 options", () => {
       return assert.throws(
         () => {
-          const opt = new OptionManager(new Logger(null, "unknown"));
+          const opt = new OptionManager();
           opt.init({
             "randomOption": true,
           });
@@ -29,7 +28,7 @@ describe("option-manager", () => {
     it("throws for removed babel 5 options", () => {
       return assert.throws(
         () => {
-          const opt = new OptionManager(new Logger(null, "unknown"));
+          const opt = new OptionManager();
           opt.init({
             "auxiliaryComment": true,
             "blacklist": true,
@@ -43,7 +42,7 @@ describe("option-manager", () => {
     it("throws for resolved but erroring preset", () => {
       return assert.throws(
         () => {
-          const opt = new OptionManager(new Logger(null, "unknown"));
+          const opt = new OptionManager();
           opt.init({
             "presets": [path.join(__dirname, "fixtures/option-manager/not-a-preset")],
           });
@@ -56,7 +55,7 @@ describe("option-manager", () => {
   describe("presets", function () {
     function presetTest(name) {
       it(name, function () {
-        const opt = new OptionManager(new Logger(null, "unknown"));
+        const opt = new OptionManager();
         const options = opt.init({
           "presets": [path.join(__dirname, "fixtures/option-manager/presets", name)],
         });
@@ -68,7 +67,7 @@ describe("option-manager", () => {
 
     function presetThrowsTest(name, msg) {
       it(name, function () {
-        const opt = new OptionManager(new Logger(null, "unknown"));
+        const opt = new OptionManager();
         assert.throws(() => opt.init({
           "presets": [path.join(__dirname, "fixtures/option-manager/presets", name)],
         }), msg);