diff --git a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/context/config/ConfigFileApplicationListener.java b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/context/config/ConfigFileApplicationListener.java
index 92584ec1d37..62a61f77d45 100644
--- a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/context/config/ConfigFileApplicationListener.java
+++ b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/context/config/ConfigFileApplicationListener.java
@@ -22,6 +22,7 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Deque;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.LinkedList;
@@ -656,27 +657,35 @@ public class ConfigFileApplicationListener
 
 		private void addLoadedPropertySources() {
 			MutablePropertySources destination = this.environment.getPropertySources();
-			String lastAdded = null;
 			List<MutablePropertySources> loaded = new ArrayList<>(this.loaded.values());
 			Collections.reverse(loaded);
+			String lastAdded = null;
+			Set<String> added = new HashSet<>();
 			for (MutablePropertySources sources : loaded) {
 				for (PropertySource<?> source : sources) {
-					if (lastAdded == null) {
-						if (destination.contains(DEFAULT_PROPERTIES)) {
-							destination.addBefore(DEFAULT_PROPERTIES, source);
-						}
-						else {
-							destination.addLast(source);
-						}
+					if (added.add(source.getName())) {
+						addLoadedPropertySource(destination, lastAdded, source);
+						lastAdded = source.getName();
 					}
-					else {
-						destination.addAfter(lastAdded, source);
-					}
-					lastAdded = source.getName();
 				}
 			}
 		}
 
+		private void addLoadedPropertySource(MutablePropertySources destination,
+				String lastAdded, PropertySource<?> source) {
+			if (lastAdded == null) {
+				if (destination.contains(DEFAULT_PROPERTIES)) {
+					destination.addBefore(DEFAULT_PROPERTIES, source);
+				}
+				else {
+					destination.addLast(source);
+				}
+			}
+			else {
+				destination.addAfter(lastAdded, source);
+			}
+		}
+
 	}
 
 	/**
diff --git a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/context/config/ConfigFileApplicationListenerTests.java b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/context/config/ConfigFileApplicationListenerTests.java
index e0be4d14625..1d82d42e113 100644
--- a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/context/config/ConfigFileApplicationListenerTests.java
+++ b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/context/config/ConfigFileApplicationListenerTests.java
@@ -900,7 +900,18 @@ public class ConfigFileApplicationListenerTests {
 		this.context = application.run("--spring.config.name=applicationloop");
 		ConfigurableEnvironment environment = this.context.getEnvironment();
 		assertThat(environment.acceptsProfiles("loop")).isTrue();
+	}
 
+	@Test
+	public void multiValueSpringProfiles() {
+		// gh-13362
+		SpringApplication application = new SpringApplication(Config.class);
+		application.setWebApplicationType(WebApplicationType.NONE);
+		this.context = application.run("--spring.config.name=applicationmultiprofiles");
+		ConfigurableEnvironment environment = this.context.getEnvironment();
+		assertThat(environment.acceptsProfiles("test")).isTrue();
+		assertThat(environment.acceptsProfiles("another-test")).isTrue();
+		assertThat(environment.getProperty("message")).isEqualTo("multiprofile");
 	}
 
 	private Condition<ConfigurableEnvironment> matchingPropertySource(
diff --git a/spring-boot-project/spring-boot/src/test/resources/applicationmultiprofiles.yml b/spring-boot-project/spring-boot/src/test/resources/applicationmultiprofiles.yml
new file mode 100644
index 00000000000..bf406504019
--- /dev/null
+++ b/spring-boot-project/spring-boot/src/test/resources/applicationmultiprofiles.yml
@@ -0,0 +1,6 @@
+spring.profiles.active: test, another-test
+message: default
+---
+spring:
+  profiles: test,another-test
+message: multiprofile