diff --git a/spring-boot-project/spring-boot-test/src/main/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunner.java b/spring-boot-project/spring-boot-test/src/main/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunner.java
index 567960a5161..e149fd66ac8 100644
--- a/spring-boot-project/spring-boot-test/src/main/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunner.java
+++ b/spring-boot-project/spring-boot-test/src/main/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunner.java
@@ -196,9 +196,8 @@ public abstract class AbstractApplicationContextRunner<SELF extends AbstractAppl
 	}
 
 	/**
-	 * Customize the {@link ClassLoader} that the {@link ApplicationContext} should use.
-	 * Customizing the {@link ClassLoader} is an effective manner to hide resources from
-	 * the classpath.
+	 * Customize the {@link ClassLoader} that the {@link ApplicationContext} should use
+	 * for resource loading and bean class loading.
 	 * @param classLoader the classloader to use (can be null to use the default)
 	 * @return a new instance with the updated class loader
 	 * @see FilteredClassLoader
@@ -274,15 +273,34 @@ public abstract class AbstractApplicationContextRunner<SELF extends AbstractAppl
 	 */
 	@SuppressWarnings("unchecked")
 	public SELF run(ContextConsumer<? super A> consumer) {
-		this.systemProperties.applyToSystemProperties(() -> {
-			try (A context = createAssertableContext()) {
-				accept(consumer, context);
-			}
-			return null;
+		withContextClassLoader(this.classLoader, () -> {
+			this.systemProperties.applyToSystemProperties(() -> {
+				try (A context = createAssertableContext()) {
+					accept(consumer, context);
+				}
+				return null;
+			});
 		});
 		return (SELF) this;
 	}
 
+	private void withContextClassLoader(ClassLoader classLoader, Runnable action) {
+		if (classLoader == null) {
+			action.run();
+		}
+		else {
+			Thread currentThread = Thread.currentThread();
+			ClassLoader previous = currentThread.getContextClassLoader();
+			currentThread.setContextClassLoader(classLoader);
+			try {
+				action.run();
+			}
+			finally {
+				currentThread.setContextClassLoader(previous);
+			}
+		}
+	}
+
 	@SuppressWarnings("unchecked")
 	private A createAssertableContext() {
 		ResolvableType resolvableType = ResolvableType
diff --git a/spring-boot-project/spring-boot-test/src/test/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunnerTests.java b/spring-boot-project/spring-boot-test/src/test/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunnerTests.java
index 24ec3c8c7c0..0af53a03bb9 100644
--- a/spring-boot-project/spring-boot-test/src/test/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunnerTests.java
+++ b/spring-boot-project/spring-boot-test/src/test/java/org/springframework/boot/test/context/runner/AbstractApplicationContextRunnerTests.java
@@ -30,8 +30,12 @@ import org.springframework.boot.test.context.FilteredClassLoader;
 import org.springframework.boot.test.context.assertj.ApplicationContextAssertProvider;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.core.env.Environment;
+import org.springframework.core.type.AnnotatedTypeMetadata;
 import org.springframework.util.ClassUtils;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -150,7 +154,7 @@ public abstract class AbstractApplicationContextRunnerTests<T extends AbstractAp
 	}
 
 	@Test
-	public void runWithClassLoaderShouldSetClassLoader() {
+	public void runWithClassLoaderShouldSetClassLoaderOnContext() {
 		get().withClassLoader(new FilteredClassLoader(Gson.class.getPackage().getName()))
 				.run((context) -> {
 					try {
@@ -164,6 +168,14 @@ public abstract class AbstractApplicationContextRunnerTests<T extends AbstractAp
 				});
 	}
 
+	@Test
+	public void runWithClassLoaderShouldSetClassLoaderOnConditionContext() {
+		get().withClassLoader(new FilteredClassLoader(Gson.class.getPackage().getName()))
+				.withUserConfiguration(ConditionalConfig.class)
+				.run((context) -> assertThat(context)
+						.hasSingleBean(ConditionalConfig.class));
+	}
+
 	@Test
 	public void thrownRuleWorksWithCheckedException() {
 		get().run((context) -> {
@@ -209,4 +221,19 @@ public abstract class AbstractApplicationContextRunnerTests<T extends AbstractAp
 
 	}
 
+	@Configuration
+	@Conditional(FilteredClassLoaderCondition.class)
+	static class ConditionalConfig {
+
+	}
+
+	static class FilteredClassLoaderCondition implements Condition {
+
+		@Override
+		public boolean matches(ConditionContext context, AnnotatedTypeMetadata metadata) {
+			return context.getClassLoader() instanceof FilteredClassLoader;
+		}
+
+	}
+
 }