diff --git a/devtools/maven/src/main/java/io/quarkus/maven/DevMojo.java b/devtools/maven/src/main/java/io/quarkus/maven/DevMojo.java
index 40e2d4a1345f0..848cd78bedcc9 100644
--- a/devtools/maven/src/main/java/io/quarkus/maven/DevMojo.java
+++ b/devtools/maven/src/main/java/io/quarkus/maven/DevMojo.java
@@ -1139,7 +1139,9 @@ private QuarkusDevModeLauncher newLauncher(Boolean debugPortOk, String bootstrap
                     .setRemoteRepositories(repos)
                     .setWorkspaceDiscovery(true)
                     .setPreferPomsFromWorkspace(true)
-                    .setCurrentProject(project.getFile().toString());
+                    // it's important to set the base directory instead of the POM
+                    // which maybe manipulated by a plugin and stored outside the base directory
+                    .setCurrentProject(project.getBasedir().toString());
 
             // There are a couple of reasons we don't want to use the original Maven session:
             // 1) a reload could be triggered by a change in a pom.xml, in which case the Maven session might not be in sync any more with the effective POM;
diff --git a/devtools/maven/src/main/java/io/quarkus/maven/QuarkusBootstrapProvider.java b/devtools/maven/src/main/java/io/quarkus/maven/QuarkusBootstrapProvider.java
index 2af84e5146410..36bcdf8908ca3 100644
--- a/devtools/maven/src/main/java/io/quarkus/maven/QuarkusBootstrapProvider.java
+++ b/devtools/maven/src/main/java/io/quarkus/maven/QuarkusBootstrapProvider.java
@@ -87,6 +87,14 @@ static Map<Path, Model> getProjectMap(MavenSession session) {
             // activated profiles or custom extensions may have overridden the build defaults
             model.setBuild(mp.getModel().getBuild());
             projectModels.put(mp.getBasedir().toPath(), model);
+            // The Maven Model API determines the project directory as the directory containing the POM file.
+            // However, in case when plugins manipulating POMs store their results elsewhere
+            // (such as the flatten plugin storing the flattened POM under the target directory),
+            // both the base directory and the directory containing the POM file should be added to the map.
+            var pomDir = mp.getFile().getParentFile();
+            if (!pomDir.equals(mp.getBasedir())) {
+                projectModels.put(pomDir.toPath(), model);
+            }
         }
         return projectModels;
     }
diff --git a/integration-tests/maven/src/test/java/io/quarkus/maven/it/DevMojoIT.java b/integration-tests/maven/src/test/java/io/quarkus/maven/it/DevMojoIT.java
index 0628e65640f2a..787e406680290 100644
--- a/integration-tests/maven/src/test/java/io/quarkus/maven/it/DevMojoIT.java
+++ b/integration-tests/maven/src/test/java/io/quarkus/maven/it/DevMojoIT.java
@@ -62,9 +62,16 @@ protected ContinuousTestingMavenTestUtils getTestingTestUtils() {
         return new ContinuousTestingMavenTestUtils();
     }
 
+    @Test
+    public void testFlattenedPomInTargetDir() throws MavenInvocationException, IOException {
+        testDir = initProject("projects/pom-in-target-dir");
+        run(true);
+        assertThat(DevModeTestUtils.getHttpResponse("/hello")).isEqualTo("Hello from RESTEasy Reactive");
+    }
+
     @Test
     public void testConfigFactoryInAppModuleBannedInCodeGen() throws MavenInvocationException, IOException {
-        testDir = initProject("projects/codegen-config-factory", "project/codegen-config-factory-banned");
+        testDir = initProject("projects/codegen-config-factory", "projects/codegen-config-factory-banned");
         run(true);
         assertThat(DevModeTestUtils.getHttpResponse("/codegen-config/acme-config-factory")).isEqualTo("n/a");
         assertThat(DevModeTestUtils.getHttpResponse("/codegen-config/acme-config-provider")).isEqualTo("n/a");
diff --git a/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/pom.xml b/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/pom.xml
new file mode 100644
index 0000000000000..e7a2ccb3e3954
--- /dev/null
+++ b/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/pom.xml
@@ -0,0 +1,91 @@
+<?xml version="1.0"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.acme</groupId>
+  <artifactId>code-with-quarkus</artifactId>
+  <version>1.0.0-SNAPSHOT</version>
+  <properties>
+    <compiler-plugin.version>${compiler-plugin.version}</compiler-plugin.version>
+    <maven.compiler.release>11</maven.compiler.release>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+    <quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
+    <quarkus.platform.group-id>io.quarkus</quarkus.platform.group-id>
+    <quarkus.platform.version>${project.version}</quarkus.platform.version>
+  </properties>
+  <dependencyManagement>
+    <dependencies>
+      <dependency>
+        <groupId>\${quarkus.platform.group-id}</groupId>
+        <artifactId>\${quarkus.platform.artifact-id}</artifactId>
+        <version>\${quarkus.platform.version}</version>
+        <type>pom</type>
+        <scope>import</scope>
+      </dependency>
+    </dependencies>
+  </dependencyManagement>
+  <dependencies>
+    <dependency>
+      <groupId>io.quarkus</groupId>
+      <artifactId>quarkus-resteasy-reactive</artifactId>
+    </dependency>
+  </dependencies>
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>flatten-maven-plugin</artifactId>
+        <version>1.5.0</version>
+        <configuration>
+          <outputDirectory>target</outputDirectory>
+          <pomElements>
+            <build>keep</build>
+            <dependencyManagement>keep</dependencyManagement>
+            <properties>keep</properties>
+          </pomElements>
+        </configuration>
+        <executions>
+          <execution>
+            <id>flatten</id>
+            <phase>process-resources</phase>
+            <goals>
+              <goal>flatten</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>flatten.clean</id>
+            <phase>clean</phase>
+            <goals>
+              <goal>clean</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>\${quarkus.platform.group-id}</groupId>
+        <artifactId>quarkus-maven-plugin</artifactId>
+        <version>\${quarkus.platform.version}</version>
+        <extensions>true</extensions>
+        <executions>
+          <execution>
+            <goals>
+              <goal>build</goal>
+              <goal>generate-code</goal>
+              <goal>generate-code-tests</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>\${compiler-plugin.version}</version>
+        <configuration>
+          <compilerArgs>
+            <arg>-parameters</arg>
+          </compilerArgs>
+        </configuration>
+      </plugin>
+    </plugins>
+  </build>
+</project>
diff --git a/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/src/main/java/org/acme/GreetingResource.java b/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/src/main/java/org/acme/GreetingResource.java
new file mode 100644
index 0000000000000..6938062ec8ff7
--- /dev/null
+++ b/integration-tests/maven/src/test/resources-filtered/projects/pom-in-target-dir/src/main/java/org/acme/GreetingResource.java
@@ -0,0 +1,16 @@
+package org.acme;
+
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+
+@Path("/hello")
+public class GreetingResource {
+
+    @GET
+    @Produces(MediaType.TEXT_PLAIN)
+    public String hello() {
+        return "Hello from RESTEasy Reactive";
+    }
+}