diff --git a/spring-boot/src/main/java/org/springframework/boot/BeanDefinitionLoader.java b/spring-boot/src/main/java/org/springframework/boot/BeanDefinitionLoader.java
index 2c07c7c42e3..989e1ca1174 100644
--- a/spring-boot/src/main/java/org/springframework/boot/BeanDefinitionLoader.java
+++ b/spring-boot/src/main/java/org/springframework/boot/BeanDefinitionLoader.java
@@ -155,7 +155,8 @@ class BeanDefinitionLoader {
 
 	private int load(CharSequence source) {
 		try {
-			return load(Class.forName(source.toString()));
+			// Use class utils so that period separated nested class names work
+			return load(ClassUtils.forName(source.toString(), null));
 		}
 		catch (ClassNotFoundException ex) {
 			// swallow exception and continue
diff --git a/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java b/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
index 5e9d0b3794f..5eb6e97418b 100644
--- a/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
+++ b/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
@@ -161,6 +161,8 @@ public class SpringApplication {
 
 	private String[] defaultCommandLineArgs;
 
+	private boolean sourcesInitialized = false;
+
 	/**
 	 * Crate a new {@link SpringApplication} instance. The application context will load
 	 * beans from the specified sources (see {@link SpringApplication class-level}
@@ -190,7 +192,8 @@ public class SpringApplication {
 	}
 
 	private void initialize(Object[] sources) {
-		if (sources != null) {
+		if (sources != null && sources.length > 0) {
+			this.sourcesInitialized = true;
 			this.sources.addAll(Arrays.asList(sources));
 		}
 		this.webEnvironment = deduceWebEnvironment();
@@ -576,6 +579,9 @@ public class SpringApplication {
 	 * @see #SpringApplication(Object...)
 	 */
 	public void setSources(Set<Object> sources) {
+		if (this.sourcesInitialized) {
+			return;
+		}
 		Assert.notNull(sources, "Sources must not be null");
 		this.sources = new LinkedHashSet<Object>(sources);
 	}
diff --git a/spring-boot/src/test/java/org/springframework/boot/OverrideSourcesTests.java b/spring-boot/src/test/java/org/springframework/boot/OverrideSourcesTests.java
new file mode 100644
index 00000000000..f31b78badd4
--- /dev/null
+++ b/spring-boot/src/test/java/org/springframework/boot/OverrideSourcesTests.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2012-2013 the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.springframework.boot;
+
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+
+import static org.junit.Assert.assertEquals;
+
+/**
+ * @author Dave Syer
+ */
+public class OverrideSourcesTests {
+
+	@Test
+	public void beanInjectedToMainConfiguration() {
+		ApplicationContext context = SpringApplication.run(
+				new Object[] { MainConfiguration.class },
+				new String[] { "--spring.main.web_environment=false" });
+		assertEquals("foo", context.getBean(Service.class).bean.name);
+	}
+
+	@Test
+	public void primaryBeanInjectedProvingSourcesNotOverridden() {
+		ApplicationContext context = SpringApplication
+				.run(new Object[] { MainConfiguration.class, TestConfiguration.class },
+						new String[] { "--spring.main.web_environment=false",
+								"--spring.main.sources=org.springframework.boot.OverrideSourcesTests.MainConfiguration" });
+		assertEquals("bar", context.getBean(Service.class).bean.name);
+	}
+
+	@Configuration
+	protected static class TestConfiguration {
+
+		@Bean
+		@Primary
+		public TestBean another() {
+			return new TestBean("bar");
+		}
+
+	}
+
+	@Configuration
+	protected static class MainConfiguration {
+
+		@Bean
+		public TestBean first() {
+			return new TestBean("foo");
+		}
+
+		@Bean
+		public Service Service() {
+			return new Service();
+		}
+
+	}
+
+	protected static class Service {
+		@Autowired
+		private TestBean bean;
+	}
+
+	protected static class TestBean {
+
+		private String name;
+
+		public TestBean(String name) {
+			this.name = name;
+		}
+
+	}
+}