diff --git a/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/NativeImagePlugin.java b/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/NativeImagePlugin.java
index 2ad7ad8d7..a86965ecf 100644
--- a/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/NativeImagePlugin.java
+++ b/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/NativeImagePlugin.java
@@ -41,6 +41,7 @@
 
 package org.graalvm.buildtools.gradle;
 
+import java.util.List;
 import org.graalvm.buildtools.VersionInfo;
 import org.graalvm.buildtools.gradle.dsl.AgentConfiguration;
 import org.graalvm.buildtools.gradle.dsl.GraalVMExtension;
@@ -74,6 +75,7 @@
 import org.gradle.api.file.DuplicatesStrategy;
 import org.gradle.api.file.FileCollection;
 import org.gradle.api.file.FileSystemLocation;
+import org.gradle.api.internal.provider.AbstractMinimalProvider;
 import org.gradle.api.model.ObjectFactory;
 import org.gradle.api.plugins.ApplicationPlugin;
 import org.gradle.api.plugins.JavaApplication;
@@ -97,7 +99,9 @@
 
 import javax.inject.Inject;
 import java.io.File;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Locale;
 import java.util.Map;
 import java.util.concurrent.Callable;
@@ -507,7 +511,7 @@ private static void configureAgent(Project project,
         AgentCommandLineProvider cliProvider = project.getObjects().newInstance(AgentCommandLineProvider.class);
         Provider<Boolean> agent = agents.get(nativeImageOptions.getName());
         cliProvider.getEnabled().set(agent);
-        Provider<Directory> outputDir = project.getLayout().getBuildDirectory().dir(AGENT_OUTPUT_FOLDER + "/" + instrumentedTask.getName());
+        Provider<Directory> outputDir = agentOutputDirectoryFor(project, nativeImageOptions, instrumentedTask);
         cliProvider.getOutputDirectory().set(outputDir);
         cliProvider.getAgentOptions().set(nativeImageOptions.getAgent().getOptions());
         instrumentedTask.get().getJvmArgumentProviders().add(cliProvider);
@@ -528,6 +532,37 @@ private static void configureAgent(Project project,
         nativeImageOptions.getConfigurationFileDirectories().from(files);
     }
 
+    private static Provider<Directory> agentOutputDirectoryFor(Project project, NativeImageOptions nativeImageOptions, TaskProvider<? extends JavaForkOptions> instrumentedTask) {
+        return new AbstractMinimalProvider<Directory>() {
+            @Override
+            public Class<Directory> getType() {
+                return Directory.class;
+            }
+
+            @Override
+            protected Value<? extends Directory> calculateOwnValue(ValueConsumer consumer) {
+                final List<String> options = nativeImageOptions.getAgent().getOptions().getOrElse(Collections.emptyList());
+                final String outputDirUnresolved = new ArrayList<>(options).stream()
+                    .filter(option -> option.startsWith("config-output-dir"))
+                    .findFirst()
+                    .map(option -> {
+                        final int firstEqualsPos = option.indexOf('=');
+                        if (firstEqualsPos == -1) {
+                            throw new IllegalArgumentException("agent option 'config-output-dir' is missing its value assignment '=...'.");
+                        }
+                        final String path = option.substring(firstEqualsPos + 1).trim();
+                        if (path.isEmpty()) {
+                            throw new IllegalArgumentException("value of agent option 'config-output-dir' must not be empty.");
+                        }
+                        return path;
+                    })
+                    .orElse(AGENT_OUTPUT_FOLDER + "/" + instrumentedTask.getName());
+
+                return Value.of(project.getLayout().getBuildDirectory().dir(outputDirUnresolved).get());
+            }
+        };
+    }
+
     private static void injectTestPluginDependencies(Project project, Property<Boolean> testSupportEnabled) {
         project.afterEvaluate(p -> {
             if (testSupportEnabled.get()) {
diff --git a/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/internal/AgentCommandLineProvider.java b/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/internal/AgentCommandLineProvider.java
index b5e77e7bf..3d7ce05eb 100644
--- a/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/internal/AgentCommandLineProvider.java
+++ b/native-gradle-plugin/src/main/java/org/graalvm/buildtools/gradle/internal/AgentCommandLineProvider.java
@@ -79,10 +79,14 @@ public Iterable<String> asArguments() {
         if (getEnabled().get()) {
             File outputDir = getOutputDirectory().getAsFile().get();
             List<String> agentOptions = new ArrayList<>(getAgentOptions().getOrElse(Collections.emptyList()));
-            if (agentOptions.stream().map(s -> s.split("=")[0]).anyMatch(s -> s.contains("config-output-dir"))) {
-                throw new IllegalStateException("config-output-dir cannot be supplied as an agent option");
+
+            // Do not add config-output-dir when a conflicting option is already present. Otherwise, this happens:
+            // native-image-agent: can only once specify exactly one of trace-output=, config-output-dir= or config-merge-dir=.
+            final List<String> mutuallyExclusiveOptions = Arrays.asList("config-output-dir", "trace-output", "config-merge-dir");
+            if (agentOptions.stream().allMatch(option -> mutuallyExclusiveOptions.stream().noneMatch(option::startsWith))) {
+                agentOptions.add("config-output-dir=" + outputDir.getAbsolutePath());
             }
-            agentOptions.add("config-output-dir=" + outputDir.getAbsolutePath());
+
             return Arrays.asList(
                     "-agentlib:native-image-agent=" + String.join(",", agentOptions),
                     "-Dorg.graalvm.nativeimage.imagecode=agent"
diff --git a/native-maven-plugin/src/main/java/org/graalvm/buildtools/maven/NativeExtension.java b/native-maven-plugin/src/main/java/org/graalvm/buildtools/maven/NativeExtension.java
index 8699343a8..81bca9f07 100644
--- a/native-maven-plugin/src/main/java/org/graalvm/buildtools/maven/NativeExtension.java
+++ b/native-maven-plugin/src/main/java/org/graalvm/buildtools/maven/NativeExtension.java
@@ -41,6 +41,8 @@
 
 package org.graalvm.buildtools.maven;
 
+import static org.graalvm.buildtools.utils.SharedConstants.AGENT_OUTPUT_FOLDER;
+
 import org.apache.maven.AbstractMavenLifecycleParticipant;
 import org.apache.maven.MavenExecutionException;
 import org.apache.maven.execution.MavenSession;
@@ -55,6 +57,7 @@
 
 import java.io.File;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.function.BiConsumer;
@@ -85,12 +88,35 @@ static String testIdsDirectory(String baseDir) {
 
     static String buildAgentArgument(String baseDir, Context context, List<String> agentOptions) {
         List<String> options = new ArrayList<>(agentOptions);
-        options.add("config-output-dir=" + agentOutputDirectoryFor(baseDir, context));
+        // Do not add config-output-dir when a conflicting option is already present. Otherwise, this happens:
+        // native-image-agent: can only once specify exactly one of trace-output=, config-output-dir= or config-merge-dir=.
+        final List<String> mutuallyExclusiveOptions = Arrays.asList("config-output-dir", "trace-output", "config-merge-dir");
+        if (agentOptions.stream().allMatch(option -> mutuallyExclusiveOptions.stream().noneMatch(option::startsWith))) {
+            options.add("config-output-dir=" + agentDefaultOutputDirectoryFor(baseDir, context));
+         }
         return "-agentlib:native-image-agent=" + String.join(",", options);
     }
 
-    private static String agentOutputDirectoryFor(String baseDir, Context context) {
-        return (baseDir + "/native/agent-output/" + context).replace('/', File.separatorChar);
+    private static String agentDefaultOutputDirectoryFor(String baseDir, Context context) {
+        return (baseDir + "/" + AGENT_OUTPUT_FOLDER + "/" + context).replace('/', File.separatorChar);
+    }
+
+    private static String agentOutputDirectoryFor(List<String> agentOptions, String baseDir, Context context) {
+        return agentOptions.stream()
+            .filter(option -> option.startsWith("config-output-dir"))
+            .findFirst()
+            .map(option -> {
+                int firstEqualsPos = option.indexOf('=');
+                if (firstEqualsPos == -1) {
+                    throw new IllegalArgumentException("agent option 'config-output-dir' is missing its value assignment '=...'.");
+                }
+                final String path = option.substring(firstEqualsPos + 1).trim();
+                if (path.isEmpty()) {
+                    throw new IllegalArgumentException("value of agent option 'config-output-dir' must not be empty.");
+                }
+                return path;
+            })
+            .orElseGet(() -> agentDefaultOutputDirectoryFor(baseDir, context));
     }
 
     @Override
@@ -114,6 +140,7 @@ public void afterProjectsRead(MavenSession session) throws MavenExecutionExcepti
 
                 // Main configuration
                 if (isAgentEnabled) {
+                    List<String> agentOptions = getAgentOptions(nativePlugin, Context.main, selectedOptionsName);
                     withPlugin(build, "exec-maven-plugin", execPlugin ->
                             updatePluginConfiguration(execPlugin, (exec, config) -> {
                                 if ("java-agent".equals(exec.getId())) {
@@ -127,7 +154,6 @@ public void afterProjectsRead(MavenSession session) throws MavenExecutionExcepti
 
                                     // Agent argument
                                     Xpp3Dom arg = new Xpp3Dom("argument");
-                                    List<String> agentOptions = getAgentOptions(nativePlugin, Context.main, selectedOptionsName);
                                     arg.setValue(buildAgentArgument(target, Context.main, agentOptions));
                                     children.add(0, arg);
 
@@ -151,7 +177,7 @@ public void afterProjectsRead(MavenSession session) throws MavenExecutionExcepti
                     updatePluginConfiguration(nativePlugin, (exec, configuration) -> {
                         Context context = exec.getGoals().stream().anyMatch("test"::equals) ? Context.test : Context.main;
                         Xpp3Dom agentResourceDirectory = findOrAppend(configuration, "agentResourceDirectory");
-                        agentResourceDirectory.setValue(agentOutputDirectoryFor(target, context));
+                        agentResourceDirectory.setValue(agentOutputDirectoryFor(agentOptions, target, context));
                     });
                 }
             });
@@ -242,11 +268,7 @@ private static List<String> getAgentOptions(Plugin nativePlugin, Context context
 
     private static void processOptionNodes(Xpp3Dom options, List<String> optionsList) {
         for (Xpp3Dom option : options.getChildren("option")) {
-            String value = assertNotEmptyAndTrim(option.getValue(), "<option> must declare a value");
-            if (value.contains("config-output-dir")) {
-                throw new IllegalStateException("config-output-dir cannot be supplied as an agent option");
-            }
-            optionsList.add(value);
+            optionsList.add(assertNotEmptyAndTrim(option.getValue(), "<option> must declare a value"));
         }
     }