diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/AutoConfigurationSorter.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/AutoConfigurationSorter.java
index 5229834e722..271fc11087d 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/AutoConfigurationSorter.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/AutoConfigurationSorter.java
@@ -20,11 +20,13 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeSet;
 
 import org.springframework.core.type.AnnotationMetadata;
 import org.springframework.core.type.classreading.MetadataReader;
@@ -53,12 +55,14 @@ class AutoConfigurationSorter {
 	}
 
 	List<String> getInPriorityOrder(Collection<String> classNames) {
+		// Initially sort alphabetically
+		List<String> alphabeticallyOrderedClassNames = new ArrayList<>(classNames);
+		Collections.sort(alphabeticallyOrderedClassNames);
+		// Then sort by order
 		AutoConfigurationClasses classes = new AutoConfigurationClasses(this.metadataReaderFactory,
-				this.autoConfigurationMetadata, classNames);
+				this.autoConfigurationMetadata, alphabeticallyOrderedClassNames);
 		List<String> orderedClassNames = new ArrayList<>(classNames);
-		// Initially sort alphabetically
 		Collections.sort(orderedClassNames);
-		// Then sort by order
 		orderedClassNames.sort((o1, o2) -> {
 			int i1 = classes.get(o1).getOrder();
 			int i2 = classes.get(o2).getOrder();
@@ -87,7 +91,9 @@ class AutoConfigurationSorter {
 			current = toSort.remove(0);
 		}
 		processing.add(current);
-		for (String after : classes.getClassesRequestedAfter(current)) {
+		Set<String> afters = new TreeSet<>(Comparator.comparing(toSort::indexOf));
+		afters.addAll(classes.getClassesRequestedAfter(current));
+		for (String after : afters) {
 			checkForCycles(processing, current, after);
 			if (!sorted.contains(after) && toSort.contains(after)) {
 				doSortByAfterAnnotation(classes, toSort, sorted, processing, after);
@@ -104,7 +110,7 @@ class AutoConfigurationSorter {
 
 	private static class AutoConfigurationClasses {
 
-		private final Map<String, AutoConfigurationClass> classes = new HashMap<>();
+		private final Map<String, AutoConfigurationClass> classes = new LinkedHashMap<>();
 
 		AutoConfigurationClasses(MetadataReaderFactory metadataReaderFactory,
 				AutoConfigurationMetadata autoConfigurationMetadata, Collection<String> classNames) {
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/AutoConfigurationSorterTests.java b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/AutoConfigurationSorterTests.java
index 6f00a402485..b9bb92d4663 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/AutoConfigurationSorterTests.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/AutoConfigurationSorterTests.java
@@ -46,6 +46,7 @@ import static org.mockito.Mockito.mock;
  * @author Phillip Webb
  * @author Andy Wilkinson
  * @author Moritz Halbritter
+ * @author Alexandre Baron
  */
 class AutoConfigurationSorterTests {
 
@@ -206,6 +207,17 @@ class AutoConfigurationSorterTests {
 			.withMessageContaining("AutoConfigure cycle detected");
 	}
 
+	@Test // gh-38904
+	void byBeforeAnnotationThenOrderAnnotation() {
+		String oa = OrderAutoConfigureA.class.getName();
+		String oa1 = OrderAutoConfigureASeedR1.class.getName();
+		String oa2 = OrderAutoConfigureASeedY2.class.getName();
+		String oa3 = OrderAutoConfigureASeedA3.class.getName();
+		String oa4 = OrderAutoConfigureAutoConfigureASeedG4.class.getName();
+		List<String> actual = this.sorter.getInPriorityOrder(Arrays.asList(oa4, oa3, oa2, oa1, oa));
+		assertThat(actual).containsExactly(oa1, oa2, oa3, oa4, oa);
+	}
+
 	private AutoConfigurationMetadata getAutoConfigurationMetadata(String... classNames) throws Exception {
 		Properties properties = new Properties();
 		for (String className : classNames) {
@@ -348,6 +360,36 @@ class AutoConfigurationSorterTests {
 
 	}
 
+	static class OrderAutoConfigureA {
+
+	}
+
+	// Use seeds in auto-configuration class names to mislead the sort by names done in
+	// AutoConfigurationSorter class.
+	@AutoConfigureBefore(OrderAutoConfigureA.class)
+	@AutoConfigureOrder(1)
+	static class OrderAutoConfigureASeedR1 {
+
+	}
+
+	@AutoConfigureBefore(OrderAutoConfigureA.class)
+	@AutoConfigureOrder(2)
+	static class OrderAutoConfigureASeedY2 {
+
+	}
+
+	@AutoConfigureBefore(OrderAutoConfigureA.class)
+	@AutoConfigureOrder(3)
+	static class OrderAutoConfigureASeedA3 {
+
+	}
+
+	@AutoConfigureBefore(OrderAutoConfigureA.class)
+	@AutoConfigureOrder(4)
+	static class OrderAutoConfigureAutoConfigureASeedG4 {
+
+	}
+
 	static class SkipCycleMetadataReaderFactory extends CachingMetadataReaderFactory {
 
 		@Override