diff --git a/src/vs/workbench/services/configuration/node/configurationEditingService.ts b/src/vs/workbench/services/configuration/node/configurationEditingService.ts
index 4352bd113b1fc..74dc243d50645 100644
--- a/src/vs/workbench/services/configuration/node/configurationEditingService.ts
+++ b/src/vs/workbench/services/configuration/node/configurationEditingService.ts
@@ -11,6 +11,7 @@ import URI from 'vs/base/common/uri';
 import * as json from 'vs/base/common/json';
 import * as encoding from 'vs/base/node/encoding';
 import * as pfs from 'vs/base/node/pfs';
+import strings = require('vs/base/common/strings');
 import {getConfigurationKeys} from 'vs/platform/configuration/common/model';
 import {IWorkbenchEditorService} from 'vs/workbench/services/editor/common/editorService';
 import {setProperty} from 'vs/base/common/jsonEdit';
@@ -72,7 +73,7 @@ export class ConfigurationEditingService implements IConfigurationEditingService
 			return ensureConfigurationFile.then(() => {
 
 				// Apply all edits to the configuration file
-				const result = this.applyEdits(contents, [operation]);
+				const result = this.applyEdits(contents, operation);
 
 				return pfs.writeFile(resource.fsPath, result, encoding.UTF8).then(() => {
 
@@ -119,17 +120,20 @@ export class ConfigurationEditingService implements IConfigurationEditingService
 		}
 	}
 
-	private applyEdits(content: string, values: IConfigurationValue[]): string {
+	private applyEdits(content: string, edit: IConfigurationEditOperation): string {
 		const {tabSize, insertSpaces} = this.configurationService.getConfiguration<{ tabSize: number; insertSpaces: boolean }>('editor');
 		const {eol} = this.configurationService.getConfiguration<{ eol: string }>('files');
 
-		while (values.length > 0) {
-			const {key, value} = values.pop();
+		const {key, value} = edit;
 
-			const edits = setProperty(content, [key], value, { tabSize, insertSpaces, eol });
-			content = applyEdits(content, edits);
+		// Without key, the entire settings file is being replaced, so we just use JSON.stringify
+		if (!key) {
+			return JSON.stringify(value, null, insertSpaces ? strings.repeat(' ', tabSize) : '\t');
 		}
 
+		const edits = setProperty(content, [key], value, { tabSize, insertSpaces, eol });
+		content = applyEdits(content, edits);
+
 		return content;
 	}
 
@@ -188,9 +192,15 @@ export class ConfigurationEditingService implements IConfigurationEditingService
 			const standaloneConfigurationKeys = Object.keys(WORKSPACE_STANDALONE_CONFIGURATIONS);
 			for (let i = 0; i < standaloneConfigurationKeys.length; i++) {
 				const key = standaloneConfigurationKeys[i];
-				const keyPrefix = `${key}.`;
 				const target = this.contextService.toResource(WORKSPACE_STANDALONE_CONFIGURATIONS[key]);
 
+				// Check for prefix
+				if (config.key === key) {
+					return { key: '', value: config.value, target, isWorkspaceStandalone: true };
+				}
+
+				// Check for prefix.<setting>
+				const keyPrefix = `${key}.`;
 				if (config.key.indexOf(keyPrefix) === 0) {
 					return { key: config.key.substr(keyPrefix.length), value: config.value, target, isWorkspaceStandalone: true };
 				}
diff --git a/src/vs/workbench/services/configuration/test/node/configurationEditingService.test.ts b/src/vs/workbench/services/configuration/test/node/configurationEditingService.test.ts
index 99f25de5b4e3a..fc2b05163a344 100644
--- a/src/vs/workbench/services/configuration/test/node/configurationEditingService.test.ts
+++ b/src/vs/workbench/services/configuration/test/node/configurationEditingService.test.ts
@@ -112,7 +112,7 @@ suite('WorkspaceConfigurationEditingService - Node', () => {
 		createWorkspace((workspaceDir, globalSettingsFile, cleanUp) => {
 			return createServices(workspaceDir, globalSettingsFile, false, true /* no workspace */).then(services => {
 				return services.configurationEditingService.writeConfiguration(ConfigurationTarget.WORKSPACE, { key: 'unknown.key', value: 'value' }).then(res => {
-				}, (error:IConfigurationEditingError) => {
+				}, (error: IConfigurationEditingError) => {
 					assert.equal(error.code, ConfigurationEditingErrorCode.ERROR_UNKNOWN_KEY);
 					services.configurationService.dispose();
 					cleanUp(done);
@@ -125,7 +125,7 @@ suite('WorkspaceConfigurationEditingService - Node', () => {
 		createWorkspace((workspaceDir, globalSettingsFile, cleanUp) => {
 			return createServices(workspaceDir, globalSettingsFile).then(services => {
 				return services.configurationEditingService.writeConfiguration(ConfigurationTarget.USER, { key: 'tasks.something', value: 'value' }).then(res => {
-				}, (error:IConfigurationEditingError) => {
+				}, (error: IConfigurationEditingError) => {
 					assert.equal(error.code, ConfigurationEditingErrorCode.ERROR_INVALID_TARGET);
 					services.configurationService.dispose();
 					cleanUp(done);
@@ -251,4 +251,44 @@ suite('WorkspaceConfigurationEditingService - Node', () => {
 			});
 		});
 	});
+
+	test('write workspace standalone setting - empty file - full JSON', (done: () => void) => {
+		createWorkspace((workspaceDir, globalSettingsFile, cleanUp) => {
+			return createServices(workspaceDir, globalSettingsFile).then(services => {
+				return services.configurationEditingService.writeConfiguration(ConfigurationTarget.WORKSPACE, { key: 'tasks', value: { 'version': '1.0.0', tasks: [{ 'taskName': 'myTask' }] } }).then(res => {
+					const target = path.join(workspaceDir, WORKSPACE_STANDALONE_CONFIGURATIONS['tasks']);
+					const contents = fs.readFileSync(target).toString('utf8');
+					const parsed = json.parse(contents);
+
+					assert.equal(parsed['version'], '1.0.0');
+					assert.equal(parsed['tasks'][0]['taskName'], 'myTask');
+
+					services.configurationService.dispose();
+					cleanUp(done);
+				});
+			});
+		});
+	});
+
+	test('write workspace standalone setting - existing file - full JSON', (done: () => void) => {
+		createWorkspace((workspaceDir, globalSettingsFile, cleanUp) => {
+			return createServices(workspaceDir, globalSettingsFile).then(services => {
+				const target = path.join(workspaceDir, WORKSPACE_STANDALONE_CONFIGURATIONS['launch']);
+
+				fs.writeFileSync(target, '{ "my.super.setting": "my.super.value" }');
+
+				return services.configurationEditingService.writeConfiguration(ConfigurationTarget.WORKSPACE, { key: 'tasks', value: { 'version': '1.0.0', tasks: [{ 'taskName': 'myTask' }] } }).then(res => {
+					const target = path.join(workspaceDir, WORKSPACE_STANDALONE_CONFIGURATIONS['tasks']);
+					const contents = fs.readFileSync(target).toString('utf8');
+					const parsed = json.parse(contents);
+
+					assert.equal(parsed['version'], '1.0.0');
+					assert.equal(parsed['tasks'][0]['taskName'], 'myTask');
+
+					services.configurationService.dispose();
+					cleanUp(done);
+				});
+			});
+		});
+	});
 });
\ No newline at end of file