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 5eb6e97418b..23feed96924 100644
--- a/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
+++ b/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
@@ -135,7 +135,9 @@ public class SpringApplication {
 
 	private final Log log = LogFactory.getLog(getClass());
 
-	private Set<Object> sources = new LinkedHashSet<Object>();
+	private Set<Object> defaultSources = new LinkedHashSet<Object>();
+
+	private Set<Object> additionalSources = new LinkedHashSet<Object>();
 
 	private Class<?> mainApplicationClass;
 
@@ -161,8 +163,6 @@ 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}
@@ -193,8 +193,7 @@ public class SpringApplication {
 
 	private void initialize(Object[] sources) {
 		if (sources != null && sources.length > 0) {
-			this.sourcesInitialized = true;
-			this.sources.addAll(Arrays.asList(sources));
+			this.additionalSources.addAll(Arrays.asList(sources));
 		}
 		this.webEnvironment = deduceWebEnvironment();
 		this.initializers = new ArrayList<ApplicationContextInitializer<?>>();
@@ -249,7 +248,8 @@ public class SpringApplication {
 
 		// Call all remaining initializers
 		callEnvironmentAwareSpringApplicationInitializers(environment);
-		Assert.notEmpty(this.sources, "Sources must not be empty");
+		Set<Object> sources = assembleSources();
+		Assert.notEmpty(sources, "Sources must not be empty");
 		if (this.showBanner) {
 			printBanner();
 		}
@@ -267,12 +267,19 @@ public class SpringApplication {
 		if (this.logStartupInfo) {
 			logStartupInfo();
 		}
-		load(context, this.sources.toArray(new Object[this.sources.size()]));
+		load(context, sources.toArray(new Object[sources.size()]));
 		refresh(context);
 		runCommandLineRunners(context, args);
 		return context;
 	}
 
+	private Set<Object> assembleSources() {
+		LinkedHashSet<Object> sources = new LinkedHashSet<Object>();
+		sources.addAll(this.defaultSources);
+		sources.addAll(this.additionalSources);
+		return sources;
+	}
+
 	private void callNonEnvironmentAwareSpringApplicationInitializers() {
 		for (ApplicationContextInitializer<?> initializer : this.initializers) {
 			if (initializer instanceof SpringApplicationInitializer
@@ -354,7 +361,7 @@ public class SpringApplication {
 		Log applicationLog = getApplicationLog();
 		new StartupInfoLogger(this.mainApplicationClass).log(applicationLog);
 		if (applicationLog.isDebugEnabled()) {
-			applicationLog.debug("Sources: " + this.sources);
+			applicationLog.debug("Sources: " + this.defaultSources);
 		}
 	}
 
@@ -561,13 +568,13 @@ public class SpringApplication {
 	}
 
 	/**
-	 * Returns a mutable set of the sources that will be used to create an
-	 * ApplicationContext when {@link #run(String...)} is called.
+	 * Returns a mutable set of the sources that will be added to an ApplicationContext
+	 * when {@link #run(String...)} is called.
 	 * @return the sources the application sources.
 	 * @see #SpringApplication(Object...)
 	 */
 	public Set<Object> getSources() {
-		return this.sources;
+		return this.defaultSources;
 	}
 
 	/**
@@ -579,11 +586,8 @@ 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);
+		this.defaultSources = new LinkedHashSet<Object>(sources);
 	}
 
 	/**
diff --git a/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java b/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
index d638d9743a8..8bb6ba989f2 100644
--- a/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
+++ b/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
@@ -16,6 +16,7 @@
 
 package org.springframework.boot;
 
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicReference;
 
 import org.junit.After;
@@ -47,6 +48,7 @@ import org.springframework.core.env.StandardEnvironment;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.ResourceLoader;
 import org.springframework.mock.web.MockServletContext;
+import org.springframework.test.util.ReflectionTestUtils;
 import org.springframework.web.context.support.StaticWebApplicationContext;
 
 import static org.hamcrest.Matchers.equalTo;
@@ -268,7 +270,10 @@ public class SpringApplicationTests {
 		application.setWebEnvironment(false);
 		application.setUseMockLoader(true);
 		application.run();
-		assertThat(application.getSources().toArray(), equalTo(sources));
+		@SuppressWarnings("unchecked")
+		Set<Object> additionalSources = (Set<Object>) ReflectionTestUtils.getField(
+				application, "additionalSources");
+		assertThat(additionalSources.toArray(), equalTo(sources));
 	}
 
 	@Test