diff --git a/packages/babel-core/src/config/config-chain.js b/packages/babel-core/src/config/config-chain.js
index f160f8a253..e81ca81f74 100644
--- a/packages/babel-core/src/config/config-chain.js
+++ b/packages/babel-core/src/config/config-chain.js
@@ -527,7 +527,7 @@ function dedupDescriptors(
 ): Array<UnloadedDescriptor> {
   const map: Map<
     Function,
-    Map<string | void, { value: UnloadedDescriptor | null }>,
+    Map<string | void, { value: UnloadedDescriptor }>,
   > = new Map();
 
   const descriptors = [];
@@ -542,16 +542,12 @@ function dedupDescriptors(
       }
       let desc = nameMap.get(item.name);
       if (!desc) {
-        desc = { value: null };
+        desc = { value: item };
         descriptors.push(desc);
 
         // Treat passPerPreset presets as unique, skipping them
         // in the merge processing steps.
         if (!item.ownPass) nameMap.set(item.name, desc);
-      }
-
-      if (item.options === false) {
-        desc.value = null;
       } else {
         desc.value = item;
       }
@@ -561,7 +557,7 @@ function dedupDescriptors(
   }
 
   return descriptors.reduce((acc, desc) => {
-    if (desc.value) acc.push(desc.value);
+    acc.push(desc.value);
     return acc;
   }, []);
 }
diff --git a/packages/babel-core/src/config/full.js b/packages/babel-core/src/config/full.js
index 8892056f76..ffdb71b02d 100644
--- a/packages/babel-core/src/config/full.js
+++ b/packages/babel-core/src/config/full.js
@@ -68,15 +68,21 @@ export default function loadFullConfig(
       },
       pass: Array<Plugin>,
     ) {
-      const plugins = config.plugins.map(descriptor => {
-        return loadPluginDescriptor(descriptor, context);
-      });
-      const presets = config.presets.map(descriptor => {
-        return {
-          preset: loadPresetDescriptor(descriptor, context),
-          pass: descriptor.ownPass ? [] : pass,
-        };
-      });
+      const plugins = config.plugins.reduce((acc, descriptor) => {
+        if (descriptor.options !== false) {
+          acc.push(loadPluginDescriptor(descriptor, context));
+        }
+        return acc;
+      }, []);
+      const presets = config.presets.reduce((acc, descriptor) => {
+        if (descriptor.options !== false) {
+          acc.push({
+            preset: loadPresetDescriptor(descriptor, context),
+            pass: descriptor.ownPass ? [] : pass,
+          });
+        }
+        return acc;
+      }, []);
 
       // resolve presets
       if (presets.length > 0) {
diff --git a/packages/babel-core/src/config/item.js b/packages/babel-core/src/config/item.js
index ab9b51207e..c847df029e 100644
--- a/packages/babel-core/src/config/item.js
+++ b/packages/babel-core/src/config/item.js
@@ -71,9 +71,11 @@ class ConfigItem {
 
   /**
    * The options, if any, that were passed to the item.
-   * Mutating this will lead to undefined behavior. If you need
+   * Mutating this will lead to undefined behavior.
+   *
+   * "false" means that this item has been disabled.
    */
-  options: {} | void;
+  options: {} | void | false;
 
   /**
    * The directory that the options for this item are relative to.
@@ -103,10 +105,6 @@ class ConfigItem {
     this._descriptor = descriptor;
     Object.defineProperty(this, "_descriptor", ({ enumerable: false }: any));
 
-    if (this._descriptor.options === false) {
-      throw new Error("Assertion failure - unexpected false options");
-    }
-
     this.value = this._descriptor.value;
     this.options = this._descriptor.options;
     this.dirname = this._descriptor.dirname;
diff --git a/packages/babel-core/test/config-loading.js b/packages/babel-core/test/config-loading.js
index 65eb0c6034..d53b746b2a 100644
--- a/packages/babel-core/test/config-loading.js
+++ b/packages/babel-core/test/config-loading.js
@@ -1,4 +1,4 @@
-import loadConfig from "../lib/config";
+import loadConfig, { loadPartialConfig } from "../lib/config";
 import path from "path";
 
 describe("@babel/core config loading", () => {
@@ -36,6 +36,46 @@ describe("@babel/core config loading", () => {
     };
   }
 
+  describe("loadPartialConfig", () => {
+    it("should preserve disabled plugins in the partial config", () => {
+      const plugin = function() {
+        return {};
+      };
+
+      const opts = loadPartialConfig({
+        ...makeOpts(true),
+        babelrc: false,
+        configFile: false,
+        plugins: [[plugin, false]],
+      });
+
+      expect(opts.options.plugins.length).toBe(1);
+      const item = opts.options.plugins[0];
+
+      expect(item.value).toBe(plugin);
+      expect(item.options).toBe(false);
+    });
+
+    it("should preserve disabled presets in the partial config", () => {
+      const preset = function() {
+        return {};
+      };
+
+      const opts = loadPartialConfig({
+        ...makeOpts(true),
+        babelrc: false,
+        configFile: false,
+        presets: [[preset, false]],
+      });
+
+      expect(opts.options.presets.length).toBe(1);
+      const item = opts.options.presets[0];
+
+      expect(item.value).toBe(preset);
+      expect(item.options).toBe(false);
+    });
+  });
+
   describe("config file", () => {
     it("should load and cache the config with plugins and presets", () => {
       const opts = makeOpts();