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 4a8e28c3a9..f1709cb5b2 100644
--- a/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
+++ b/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
@@ -70,6 +70,7 @@ import org.springframework.core.io.ResourceLoader;
 import org.springframework.core.io.support.SpringFactoriesLoader;
 import org.springframework.util.Assert;
 import org.springframework.util.ClassUtils;
+import org.springframework.util.CollectionUtils;
 import org.springframework.util.ObjectUtils;
 import org.springframework.util.ReflectionUtils;
 import org.springframework.util.StopWatch;
@@ -213,9 +214,9 @@ public class SpringApplication {
 
 	private static final Log logger = LogFactory.getLog(SpringApplication.class);
 
-	private final Object[] primarySources;
+	private Set<Object> primarySources;
 
-	private Set<Object> additionalSources = new LinkedHashSet<>();
+	private Set<Object> sources = new LinkedHashSet<>();
 
 	private Class<?> mainApplicationClass;
 
@@ -261,7 +262,6 @@ public class SpringApplication {
 	 */
 	public SpringApplication(Object... primarySources) {
 		initialize(primarySources);
-		this.primarySources = primarySources;
 	}
 
 	/**
@@ -277,12 +277,13 @@ public class SpringApplication {
 	 */
 	public SpringApplication(ResourceLoader resourceLoader, Object... primarySources) {
 		this.resourceLoader = resourceLoader;
-		this.primarySources = primarySources;
 		initialize(primarySources);
 	}
 
 	@SuppressWarnings({ "unchecked", "rawtypes" })
-	private void initialize(Object[] sources) {
+	private void initialize(Object[] primarySources) {
+		Assert.notNull(primarySources, "PrimarySources must not be null");
+		this.primarySources = new LinkedHashSet<>(Arrays.asList(primarySources));
 		this.webApplicationType = deduceWebApplication();
 		setInitializers((Collection) getSpringFactoriesInstances(
 				ApplicationContextInitializer.class));
@@ -1122,18 +1123,35 @@ public class SpringApplication {
 		this.environment = environment;
 	}
 
+	/**
+	 * Add additional items to the primary sources that will be added to an
+	 * ApplicationContext when {@link #run(String...)} is called.
+	 * <p>
+	 * The sources here are added to those that were set in the constructor. Most users
+	 * should consider using {@link #getSources()}/{@link #setSources(Set)} rather than
+	 * this calling method.
+	 * @param additionalPrimarySources the additional primary sources to add
+	 * @see #SpringApplication(Object...)
+	 * @see #getSources()
+	 * @see #setSources(Set)
+	 * @see #getAllSources()
+	 */
+	public void addPrimarySources(Collection<Object> additionalPrimarySources) {
+		this.primarySources.addAll(additionalPrimarySources);
+	}
+
 	/**
 	 * Returns a mutable set of the sources that will be added to an ApplicationContext
 	 * when {@link #run(String...)} is called.
 	 * <p>
 	 * Sources set here will be used in addition to any primary sources set in the
 	 * constructor.
-	 * @return the sources the application sources.
+	 * @return the application sources.
 	 * @see #SpringApplication(Object...)
 	 * @see #getAllSources()
 	 */
 	public Set<Object> getSources() {
-		return this.additionalSources;
+		return this.sources;
 	}
 
 	/**
@@ -1142,13 +1160,13 @@ public class SpringApplication {
 	 * <p>
 	 * Sources set here will be used in addition to any primary sources set in the
 	 * constructor.
-	 * @param sources the sources to set
+	 * @param sources the application sources to set
 	 * @see #SpringApplication(Object...)
 	 * @see #getAllSources()
 	 */
 	public void setSources(Set<Object> sources) {
 		Assert.notNull(sources, "Sources must not be null");
-		this.additionalSources = new LinkedHashSet<>(sources);
+		this.sources = new LinkedHashSet<>(sources);
 	}
 
 	/**
@@ -1160,10 +1178,12 @@ public class SpringApplication {
 	 */
 	public Set<Object> getAllSources() {
 		Set<Object> allSources = new LinkedHashSet<>();
-		if (!ObjectUtils.isEmpty(this.primarySources)) {
-			allSources.addAll(Arrays.asList(this.primarySources));
+		if (!CollectionUtils.isEmpty(this.primarySources)) {
+			allSources.addAll(this.primarySources);
+		}
+		if (!CollectionUtils.isEmpty(this.sources)) {
+			allSources.addAll(this.sources);
 		}
-		allSources.addAll(this.additionalSources);
 		return Collections.unmodifiableSet(allSources);
 	}
 
diff --git a/spring-boot/src/main/java/org/springframework/boot/builder/SpringApplicationBuilder.java b/spring-boot/src/main/java/org/springframework/boot/builder/SpringApplicationBuilder.java
index e31086c81d..da65d8f071 100644
--- a/spring-boot/src/main/java/org/springframework/boot/builder/SpringApplicationBuilder.java
+++ b/spring-boot/src/main/java/org/springframework/boot/builder/SpringApplicationBuilder.java
@@ -61,6 +61,7 @@ import org.springframework.core.io.ResourceLoader;
  *
  * @author Dave Syer
  * @author Andy Wilkinson
+ * @see SpringApplication
  */
 public class SpringApplicationBuilder {
 
@@ -165,7 +166,7 @@ public class SpringApplicationBuilder {
 	 */
 	public SpringApplication build(String... args) {
 		configureAsChildIfNecessary(args);
-		this.application.setSources(this.sources);
+		this.application.addPrimarySources(this.sources);
 		return this.application;
 	}
 
@@ -193,7 +194,7 @@ public class SpringApplicationBuilder {
 		bannerMode(Banner.Mode.OFF);
 
 		// Make sure sources get copied over
-		this.application.setSources(this.sources);
+		this.application.addPrimarySources(this.sources);
 
 		return child;
 	}
diff --git a/spring-boot/src/main/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializer.java b/spring-boot/src/main/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializer.java
index 940aa197e7..a51b053e5e 100644
--- a/spring-boot/src/main/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializer.java
+++ b/spring-boot/src/main/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializer.java
@@ -16,6 +16,8 @@
 
 package org.springframework.boot.web.servlet.support;
 
+import java.util.Collections;
+
 import javax.servlet.Filter;
 import javax.servlet.Servlet;
 import javax.servlet.ServletContext;
@@ -115,11 +117,11 @@ public abstract class SpringBootServletInitializer implements WebApplicationInit
 		builder.contextClass(AnnotationConfigServletWebServerApplicationContext.class);
 		builder = configure(builder);
 		SpringApplication application = builder.build();
-		if (application.getSources().isEmpty() && AnnotationUtils
+		if (application.getAllSources().isEmpty() && AnnotationUtils
 				.findAnnotation(getClass(), Configuration.class) != null) {
-			application.getSources().add(getClass());
+			application.addPrimarySources(Collections.singleton(getClass()));
 		}
-		Assert.state(!application.getSources().isEmpty(),
+		Assert.state(!application.getAllSources().isEmpty(),
 				"No SpringApplication sources have been defined. Either override the "
 						+ "configure method or add an @Configuration annotation");
 		// Ensure error pages are registered
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 fc66965f9e..7655e4a6ff 100644
--- a/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
+++ b/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
@@ -157,7 +157,7 @@ public class SpringApplicationTests {
 	@Test
 	public void sourcesMustNotBeNull() throws Exception {
 		this.thrown.expect(IllegalArgumentException.class);
-		this.thrown.expectMessage("Sources must not be empty");
+		this.thrown.expectMessage("PrimarySources must not be null");
 		new SpringApplication((Object[]) null).run();
 	}
 
diff --git a/spring-boot/src/test/java/org/springframework/boot/builder/SpringApplicationBuilderTests.java b/spring-boot/src/test/java/org/springframework/boot/builder/SpringApplicationBuilderTests.java
index 37f52fe72d..ae8fa65f9c 100644
--- a/spring-boot/src/test/java/org/springframework/boot/builder/SpringApplicationBuilderTests.java
+++ b/spring-boot/src/test/java/org/springframework/boot/builder/SpringApplicationBuilderTests.java
@@ -304,6 +304,16 @@ public class SpringApplicationBuilderTests {
 		assertThat(application.application().getInitializers()).hasSize(5);
 	}
 
+	@Test
+	public void sourcesWithBoundSources() throws Exception {
+		SpringApplicationBuilder application = new SpringApplicationBuilder()
+				.web(WebApplicationType.NONE).sources(ExampleConfig.class)
+				.properties("spring.main.sources=" + ChildConfig.class.getName());
+		this.context = application.run();
+		this.context.getBean(ExampleConfig.class);
+		this.context.getBean(ChildConfig.class);
+	}
+
 	@Configuration
 	static class ExampleConfig {
 
diff --git a/spring-boot/src/test/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializerTests.java b/spring-boot/src/test/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializerTests.java
index 4685a1b86b..016a12d829 100644
--- a/spring-boot/src/test/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializerTests.java
+++ b/spring-boot/src/test/java/org/springframework/boot/web/servlet/support/SpringBootServletInitializerTests.java
@@ -66,14 +66,14 @@ public class SpringBootServletInitializerTests {
 	public void withConfigurationAnnotation() throws Exception {
 		new WithConfigurationAnnotation()
 				.createRootApplicationContext(this.servletContext);
-		assertThat(this.application.getSources()).containsOnly(
+		assertThat(this.application.getAllSources()).containsOnly(
 				WithConfigurationAnnotation.class, ErrorPageFilterConfiguration.class);
 	}
 
 	@Test
 	public void withConfiguredSource() throws Exception {
 		new WithConfiguredSource().createRootApplicationContext(this.servletContext);
-		assertThat(this.application.getSources()).containsOnly(Config.class,
+		assertThat(this.application.getAllSources()).containsOnly(Config.class,
 				ErrorPageFilterConfiguration.class);
 	}