diff --git a/packages/plugin-ext/src/plugin/preference-registry.spec.ts b/packages/plugin-ext/src/plugin/preference-registry.spec.ts
new file mode 100644
index 0000000000000..5dea9fc44ced0
--- /dev/null
+++ b/packages/plugin-ext/src/plugin/preference-registry.spec.ts
@@ -0,0 +1,83 @@
+/********************************************************************************
+ * Copyright (C) 2020 Red Hat, Inc. and others.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Public License v. 2.0 which is available at
+ * http://www.eclipse.org/legal/epl-2.0.
+ *
+ * This Source Code may also be made available under the following Secondary
+ * Licenses when the conditions for such availability set forth in the Eclipse
+ * Public License v. 2.0 are satisfied: GNU General Public License, version 2
+ * with the GNU Classpath Exception which is available at
+ * https://www.gnu.org/software/classpath/license.html.
+ *
+ * SPDX-License-Identifier: EPL-2.0 OR GPL-2.0 WITH Classpath-exception-2.0
+ ********************************************************************************/
+
+import { PreferenceRegistryExtImpl } from './preference-registry';
+import * as chai from 'chai';
+import { WorkspaceExtImpl } from '../plugin/workspace';
+import { RPCProtocol } from '../common/rpc-protocol';
+import { ProxyIdentifier } from '../common/rpc-protocol';
+
+const expect = chai.expect;
+
+/* eslint-disable @typescript-eslint/no-explicit-any */
+describe('PreferenceRegistryExtImpl:', () => {
+
+    let preferenceRegistryExtImpl: PreferenceRegistryExtImpl;
+    const getProxy = (proxyId: ProxyIdentifier<unknown>) => { };
+    const set = (identifier: ProxyIdentifier<unknown>, instance: unknown) => { };
+    const dispose = () => { };
+
+    const mockRPC = {
+        getProxy,
+        set,
+        dispose
+
+    } as RPCProtocol;
+    const mockWorkspace: WorkspaceExtImpl = {} as WorkspaceExtImpl;
+
+    beforeEach(() => {
+        preferenceRegistryExtImpl = new PreferenceRegistryExtImpl(mockRPC, mockWorkspace);
+    });
+
+    it('Check parseConfigurationData', () => {
+        const value: { [key: string]: any } = {
+            'my.key1.foo': 'value1',
+            'my.key1.bar': 'value2',
+        };
+        const result: { [key: string]: any } = (preferenceRegistryExtImpl as any).parseConfigurationData(value);
+        expect(result.my).to.be.an('object');
+        expect(result.my.key1).to.be.an('object');
+
+        expect(result.my.key1.foo).to.be.an('string');
+        expect(result.my.key1.foo).to.equal('value1');
+
+        expect(result.my.key1.bar).to.be.an('string');
+        expect(result.my.key1.bar).to.equal('value2');
+    });
+
+    it('Prototype pollution check', () => {
+        const value: { [key: string]: any } = {
+            'my.key1.foo': 'value1',
+            '__proto__.injectedParsedPrototype': true,
+            'a.__proto__.injectedParsedPrototype': true,
+            '__proto__': {},
+        };
+        const result: { [key: string]: any } = (preferenceRegistryExtImpl as any).parseConfigurationData(value);
+        expect(result.my).to.be.an('object');
+
+        expect(result.__proto__).to.be.equal(Object.prototype);
+
+        expect(result.my.key1.foo).to.equal('value1');
+
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const prototypeObject = Object.prototype as any;
+        expect(prototypeObject.injectedParsedPrototype).to.be.an('undefined');
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const rawObject = {} as any;
+        expect(rawObject.injectedParsedPrototype).to.be.an('undefined');
+    });
+
+});
diff --git a/packages/plugin-ext/src/plugin/preference-registry.ts b/packages/plugin-ext/src/plugin/preference-registry.ts
index 06bbcfa4dfec6..52fd7ddb91adc 100644
--- a/packages/plugin-ext/src/plugin/preference-registry.ts
+++ b/packages/plugin-ext/src/plugin/preference-registry.ts
@@ -31,6 +31,8 @@ import { Configuration, ConfigurationModel } from './preferences/configuration';
 import { WorkspaceExtImpl } from './workspace';
 import cloneDeep = require('lodash.clonedeep');
 
+const prototypePropertyRe = /\b__proto__\b/;
+
 enum ConfigurationTarget {
     Global = 1,
     Workspace = 2,
@@ -238,7 +240,7 @@ export class PreferenceRegistryExtImpl implements PreferenceRegistryExt {
     private readonly OVERRIDE_PROPERTY_PATTERN = new RegExp(this.OVERRIDE_PROPERTY);
 
     private parseConfigurationData(data: { [key: string]: any }): { [key: string]: any } {
-        return Object.keys(data).reduce((result: any, key: string) => {
+        return Object.keys(data).filter(key => !prototypePropertyRe.test(key)).reduce((result: any, key: string) => {
             const parts = key.split('.');
             let branch = result;
 
diff --git a/packages/plugin-ext/src/plugin/preferences/configuration.spec.ts b/packages/plugin-ext/src/plugin/preferences/configuration.spec.ts
index b623650ea96d0..4605e30de24e6 100644
--- a/packages/plugin-ext/src/plugin/preferences/configuration.spec.ts
+++ b/packages/plugin-ext/src/plugin/preferences/configuration.spec.ts
@@ -14,6 +14,7 @@
  * SPDX-License-Identifier: EPL-2.0 OR GPL-2.0 WITH Classpath-exception-2.0
  ********************************************************************************/
 
+/* eslint-disable @typescript-eslint/no-explicit-any */
 import * as chai from 'chai';
 import { Configuration, ConfigurationModel } from './configuration';
 import { PreferenceData } from '../../common';
@@ -247,4 +248,35 @@ describe('Configuration:', () => {
 
     });
 
+    describe('ConfigurationModel', () => {
+
+        it('check merge', () => {
+            defaultConfiguration = new ConfigurationModel(
+                preferences[PreferenceScope.Default],
+                Object.keys(preferences[PreferenceScope.Default])
+            );
+            userConfiguration = new ConfigurationModel(
+                preferences[PreferenceScope.User],
+                Object.keys(preferences[PreferenceScope.User])
+            );
+            workspaceConfiguration = new ConfigurationModel(
+                preferences[PreferenceScope.Workspace],
+                Object.keys(preferences[PreferenceScope.Workspace])
+            );
+            const mergedConfiguration = new ConfigurationModel().merge(defaultConfiguration, userConfiguration, workspaceConfiguration);
+            expect(mergedConfiguration.getValue('tabSize')).to.equal(4);
+        });
+
+        it('Prototype pollution check', () => {
+            const payload = JSON.parse('{"__proto__":{"injectedConfigurationPrototype": true}}');
+            const configurationModel = new ConfigurationModel();
+            configurationModel.merge(new ConfigurationModel(payload));
+            const prototypeObject = Object.prototype as any;
+            expect(prototypeObject.injectedConfigurationPrototype).to.be.an('undefined');
+            const rawObject = {} as any;
+            expect(rawObject.injectedConfigurationPrototype).to.be.an('undefined');
+        });
+
+    });
+
 });
diff --git a/packages/plugin-ext/src/plugin/preferences/configuration.ts b/packages/plugin-ext/src/plugin/preferences/configuration.ts
index 016ad316e8846..9f5eaae3eefea 100644
--- a/packages/plugin-ext/src/plugin/preferences/configuration.ts
+++ b/packages/plugin-ext/src/plugin/preferences/configuration.ts
@@ -143,6 +143,9 @@ export class ConfigurationModel {
 
     private mergeContents(source: any, target: any): void {
         for (const key of Object.keys(target)) {
+            if (key === '__proto__') {
+                continue;
+            }
             if (key in source) {
                 if (isObject(source[key]) && isObject(target[key])) {
                     this.mergeContents(source[key], target[key]);