diff --git a/module/spring-boot-devtools/src/main/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolver.java b/module/spring-boot-devtools/src/main/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolver.java
index 7541b0947c4..27cc715ce83 100644
--- a/module/spring-boot-devtools/src/main/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolver.java
+++ b/module/spring-boot-devtools/src/main/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolver.java
@@ -33,6 +33,7 @@ import org.springframework.boot.devtools.restart.classloader.ClassLoaderFile;
 import org.springframework.boot.devtools.restart.classloader.ClassLoaderFile.Kind;
 import org.springframework.boot.devtools.restart.classloader.ClassLoaderFileURLStreamHandler;
 import org.springframework.boot.devtools.restart.classloader.ClassLoaderFiles;
+import org.springframework.boot.devtools.restart.classloader.ClassLoaderFiles.SourceDirectory;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.support.AbstractApplicationContext;
 import org.springframework.core.io.AbstractResource;
@@ -58,6 +59,7 @@ import org.springframework.web.context.support.ServletContextResourcePatternReso
  * @author Andy Wilkinson
  * @author Phillip Webb
  * @author Stephane Nicoll
+ * @author DongHoon Lee
  */
 final class ClassLoaderFilesResourcePatternResolver implements ResourcePatternResolver {
 
@@ -146,22 +148,35 @@ final class ClassLoaderFilesResourcePatternResolver implements ResourcePatternRe
 	}
 
 	private boolean isDeleted(Resource resource) {
-		for (Entry<String, ClassLoaderFile> entry : this.classLoaderFiles.getFileEntries()) {
-			try {
-				String name = entry.getKey();
-				ClassLoaderFile file = entry.getValue();
-				if (file.getKind() == Kind.DELETED && resource.exists()
-						&& resource.getURI().toString().endsWith(name)) {
+		String uri = null;
+		for (SourceDirectory sourceDirectory : this.classLoaderFiles.getSourceDirectories()) {
+			for (Entry<String, ClassLoaderFile> entry : sourceDirectory.getFilesEntrySet()) {
+				if (entry.getValue().getKind() != Kind.DELETED) {
+					continue;
+				}
+				if (uri == null) {
+					if (!resource.exists()) {
+						return false;
+					}
+					uri = getUri(resource);
+				}
+				if (uri.endsWith(entry.getKey())) {
 					return true;
 				}
 			}
-			catch (IOException ex) {
-				throw new IllegalStateException("Failed to retrieve URI from '" + resource + "'", ex);
-			}
 		}
 		return false;
 	}
 
+	private String getUri(Resource resource) {
+		try {
+			return resource.getURI().toString();
+		}
+		catch (IOException ex) {
+			throw new IllegalStateException("Failed to retrieve URI from '" + resource + "'", ex);
+		}
+	}
+
 	/**
 	 * A {@link Resource} that represents a {@link ClassLoaderFile} that has been
 	 * {@link Kind#DELETED deleted}.
diff --git a/module/spring-boot-devtools/src/test/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolverTests.java b/module/spring-boot-devtools/src/test/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolverTests.java
index 998b73c59bd..68b9ba6f6a3 100644
--- a/module/spring-boot-devtools/src/test/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolverTests.java
+++ b/module/spring-boot-devtools/src/test/java/org/springframework/boot/devtools/restart/ClassLoaderFilesResourcePatternResolverTests.java
@@ -18,6 +18,7 @@ package org.springframework.boot.devtools.restart;
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -43,6 +44,7 @@ import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.BDDMockito.given;
 import static org.mockito.BDDMockito.then;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.never;
 
 /**
  * Tests for {@link ClassLoaderFilesResourcePatternResolver}.
@@ -50,6 +52,7 @@ import static org.mockito.Mockito.mock;
  * @author Phillip Webb
  * @author Andy Wilkinson
  * @author Stephane Nicoll
+ * @author DongHoon Lee
  */
 class ClassLoaderFilesResourcePatternResolverTests {
 
@@ -90,6 +93,41 @@ class ClassLoaderFilesResourcePatternResolverTests {
 		assertThat(resource).isInstanceOf(DeletedClassLoaderFileResource.class);
 	}
 
+	@Test
+	void getResourceWhenDeletedInAnotherSourceDirectoryShouldReturnDeletedResource(@TempDir File directory)
+			throws Exception {
+		File file = createFile(directory, "name.class");
+		this.files.addFile("one", "other.class", new ClassLoaderFile(Kind.ADDED, new byte[0]));
+		this.files.addFile("two", "name.class", new ClassLoaderFile(Kind.DELETED, null));
+		Resource resource = this.resolver.getResource("file:" + file.getAbsolutePath());
+		assertThat(resource).isInstanceOf(DeletedClassLoaderFileResource.class);
+	}
+
+	@Test
+	void getResourceWhenManyFilesAreDeletedShouldCheckResourceOnlyOnce() throws Exception {
+		Resource resource = mock(Resource.class);
+		given(resource.exists()).willReturn(true);
+		given(resource.getURI()).willReturn(URI.create("file:/app/classes/three.class"));
+		this.resolver = createResolverResolving("foo:some-file.txt", resource);
+		this.files.addFile("one", "one.class", new ClassLoaderFile(Kind.DELETED, null));
+		this.files.addFile("one", "two.class", new ClassLoaderFile(Kind.DELETED, null));
+		this.files.addFile("two", "three.class", new ClassLoaderFile(Kind.DELETED, null));
+		assertThat(this.resolver.getResource("foo:some-file.txt")).isInstanceOf(DeletedClassLoaderFileResource.class);
+		then(resource).should().exists();
+		then(resource).should().getURI();
+	}
+
+	@Test
+	void getResourceWhenNoFileIsDeletedShouldNotCheckResource() throws Exception {
+		Resource resource = mock(Resource.class);
+		this.resolver = createResolverResolving("foo:some-file.txt", resource);
+		this.files.addFile("one", "one.class", new ClassLoaderFile(Kind.ADDED, new byte[0]));
+		this.files.addFile("two", "two.class", new ClassLoaderFile(Kind.MODIFIED, new byte[0]));
+		assertThat(this.resolver.getResource("foo:some-file.txt")).isSameAs(resource);
+		then(resource).should(never()).exists();
+		then(resource).should(never()).getURI();
+	}
+
 	@Test
 	void getResourcesShouldReturnResources(@TempDir File directory) throws Exception {
 		File file = createFile(directory, "name.class");
@@ -173,6 +211,12 @@ class ClassLoaderFilesResourcePatternResolverTests {
 		then(resolver).should().resolve(eq("foo:some-file.txt"), any(ResourceLoader.class));
 	}
 
+	private ClassLoaderFilesResourcePatternResolver createResolverResolving(String location, Resource resource) {
+		GenericApplicationContext context = new GenericApplicationContext();
+		context.addProtocolResolver(mockProtocolResolver(location, resource));
+		return new ClassLoaderFilesResourcePatternResolver(context, this.files);
+	}
+
 	private ProtocolResolver mockProtocolResolver(String path, Resource resource) {
 		ProtocolResolver resolver = mock(ProtocolResolver.class);
 		given(resolver.resolve(eq(path), any(ResourceLoader.class))).willReturn(resource);