diff --git a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
index 4666648570..fe2d6ac64d 100644
--- a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
+++ b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java
@@ -30,6 +30,7 @@ import java.util.Objects;
 import java.util.Optional;
 import java.util.Properties;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.stream.Stream;
 
 import org.apache.commons.logging.Log;
@@ -1457,10 +1458,10 @@ public class SpringApplication {
 		 */
 		public SpringApplication.Running run(String... args) {
 			RunListener runListener = new RunListener();
-			SpringApplicationHook hook = (springApplication) -> {
+			SpringApplicationHook hook = new SingleUseSpringApplicationHook((springApplication) -> {
 				springApplication.addPrimarySources(this.sources);
 				return runListener;
-			};
+			});
 			withHook(hook, () -> this.main.accept(args));
 			return runListener;
 		}
@@ -1580,4 +1581,21 @@ public class SpringApplication {
 
 	}
 
+	private static final class SingleUseSpringApplicationHook implements SpringApplicationHook {
+
+		private final AtomicBoolean used = new AtomicBoolean();
+
+		private final SpringApplicationHook delegate;
+
+		private SingleUseSpringApplicationHook(SpringApplicationHook delegate) {
+			this.delegate = delegate;
+		}
+
+		@Override
+		public SpringApplicationRunListener getRunListener(SpringApplication springApplication) {
+			return this.used.compareAndSet(false, true) ? this.delegate.getRunListener(springApplication) : null;
+		}
+
+	}
+
 }
diff --git a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
index 3b9d87be9b..9523dc903c 100644
--- a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
+++ b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java
@@ -24,6 +24,7 @@ import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.function.Supplier;
@@ -1363,18 +1364,30 @@ class SpringApplicationTests {
 	@Test
 	void fromRunsWithAdditionalSources() {
 		assertThat(ExampleAdditionalConfig.local.get()).isNull();
-		SpringApplication.from(ExampleFromMainMethod::main).with(ExampleAdditionalConfig.class).run();
+		this.context = SpringApplication.from(ExampleFromMainMethod::main)
+			.with(ExampleAdditionalConfig.class)
+			.run()
+			.getApplicationContext();
 		assertThat(ExampleAdditionalConfig.local.get()).isNotNull();
 		ExampleAdditionalConfig.local.set(null);
 	}
 
 	@Test
 	void fromReturnsApplicationContext() {
-		ConfigurableApplicationContext context = SpringApplication.from(ExampleFromMainMethod::main)
+		this.context = SpringApplication.from(ExampleFromMainMethod::main)
 			.with(ExampleAdditionalConfig.class)
 			.run()
 			.getApplicationContext();
-		assertThat(context).isNotNull();
+		assertThat(this.context).isNotNull();
+	}
+
+	@Test
+	void fromWithMultipleApplicationsOnlyAppliesAdditionalSourcesOnce() {
+		this.context = SpringApplication.from(MultipleApplicationsMainMethod::main)
+			.with(SingleUseAdditionalConfig.class)
+			.run()
+			.getApplicationContext();
+		assertThatNoException().isThrownBy(() -> this.context.getBean(SingleUseAdditionalConfig.class));
 	}
 
 	private <S extends AvailabilityState> ArgumentMatcher<ApplicationEvent> isAvailabilityChangeEventWithState(
@@ -1949,6 +1962,31 @@ class SpringApplicationTests {
 
 	}
 
+	static class MultipleApplicationsMainMethod {
+
+		static void main(String[] args) {
+			SpringApplication application = new SpringApplication(ExampleConfig.class);
+			application.setWebApplicationType(WebApplicationType.NONE);
+			application.addListeners(new ApplicationListener<ApplicationEnvironmentPreparedEvent>() {
+
+				@Override
+				public void onApplicationEvent(ApplicationEnvironmentPreparedEvent event) {
+					SpringApplicationBuilder builder = new SpringApplicationBuilder(
+							InnerApplicationConfiguration.class);
+					builder.web(WebApplicationType.NONE);
+					builder.run().close();
+				}
+
+			});
+			application.run(args);
+		}
+
+		static class InnerApplicationConfiguration {
+
+		}
+
+	}
+
 	@Configuration
 	static class ExampleAdditionalConfig {
 
@@ -1960,4 +1998,17 @@ class SpringApplicationTests {
 
 	}
 
+	@Configuration
+	static class SingleUseAdditionalConfig {
+
+		private static AtomicBoolean used = new AtomicBoolean(false);
+
+		SingleUseAdditionalConfig() {
+			if (!used.compareAndSet(false, true)) {
+				throw new IllegalStateException("Single-use configuration has already been used");
+			}
+		}
+
+	}
+
 }