diff --git a/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyForgeModDevPlugin.java b/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyForgeModDevPlugin.java
index a3f7ef17..2f5ebe2c 100644
--- a/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyForgeModDevPlugin.java
+++ b/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyForgeModDevPlugin.java
@@ -61,7 +61,7 @@ public void apply(Project project) {
 
         // Do not apply the repositories automatically if they have been applied at the settings-level.
         // It's still possible to apply them manually, though.
-        if (!project.getGradle().getPlugins().hasPlugin(LegacyRepositoriesPlugin.class)) {
+        if (!project.getPlugins().hasPlugin(LegacyRepositoriesPlugin.DeclaredInSettingsPlugin.class)) {
             project.getPlugins().apply(LegacyRepositoriesPlugin.class);
         } else {
             LOG.info("Not enabling legacy repositories since they were applied at the settings level");
diff --git a/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyRepositoriesPlugin.java b/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyRepositoriesPlugin.java
index 20e5d2a7..0a0bb1bf 100644
--- a/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyRepositoriesPlugin.java
+++ b/src/legacy/java/net/neoforged/moddevgradle/legacyforge/internal/LegacyRepositoriesPlugin.java
@@ -22,7 +22,9 @@ public void apply(PluginAware target) {
             applyRepositories(project.getRepositories());
         } else if (target instanceof Settings settings) {
             applyRepositories(settings.getDependencyResolutionManagement().getRepositories());
-            settings.getGradle().getPlugins().apply(getClass()); // Add a marker to Gradle
+
+            // Apply our marker plugin to all projects.
+            settings.getGradle().beforeProject(project -> project.getPluginManager().apply(DeclaredInSettingsPlugin.class));
         } else if (target instanceof Gradle gradle) {
             // Do nothing
         } else {
@@ -30,6 +32,14 @@ public void apply(PluginAware target) {
         }
     }
 
+    /**
+     * A marker plugin applied to each project, indicating this plugin was applied on the settings level.
+     */
+    public static final class DeclaredInSettingsPlugin implements Plugin<Project> {
+        @Override
+        public void apply(Project target) {}
+    }
+
     private void applyRepositories(RepositoryHandler repositories) {
         repositories.maven(repo -> {
             repo.setName("MinecraftForge");
diff --git a/src/main/java/net/neoforged/moddevgradle/internal/ModDevPlugin.java b/src/main/java/net/neoforged/moddevgradle/internal/ModDevPlugin.java
index 97f0e7f5..edd22264 100644
--- a/src/main/java/net/neoforged/moddevgradle/internal/ModDevPlugin.java
+++ b/src/main/java/net/neoforged/moddevgradle/internal/ModDevPlugin.java
@@ -30,7 +30,7 @@ public void apply(Project project) {
 
         // Do not apply the repositories automatically if they have been applied at the settings-level.
         // It's still possible to apply them manually, though.
-        if (!project.getGradle().getPlugins().hasPlugin(RepositoriesPlugin.class)) {
+        if (!project.getPlugins().hasPlugin(RepositoriesPlugin.DeclaredInSettingsPlugin.class)) {
             project.getPlugins().apply(RepositoriesPlugin.class);
         } else {
             LOG.info("Not enabling NeoForged repositories since they were applied at the settings level");
diff --git a/src/main/java/net/neoforged/moddevgradle/internal/RepositoriesPlugin.java b/src/main/java/net/neoforged/moddevgradle/internal/RepositoriesPlugin.java
index ec296a1a..47f82f4b 100644
--- a/src/main/java/net/neoforged/moddevgradle/internal/RepositoriesPlugin.java
+++ b/src/main/java/net/neoforged/moddevgradle/internal/RepositoriesPlugin.java
@@ -26,7 +26,9 @@ public void apply(PluginAware target) {
             applyRepositories(project.getRepositories());
         } else if (target instanceof Settings settings) {
             applyRepositories(settings.getDependencyResolutionManagement().getRepositories());
-            settings.getGradle().getPlugins().apply(getClass()); // Add a marker to Gradle
+
+            // Apply our marker plugin to all projects.
+            settings.getGradle().beforeProject(project -> project.getPluginManager().apply(DeclaredInSettingsPlugin.class));
         } else if (target instanceof Gradle gradle) {
             // Do nothing
         } else {
@@ -34,6 +36,14 @@ public void apply(PluginAware target) {
         }
     }
 
+    /**
+     * A marker plugin applied to each project, indicating this plugin was applied on the settings level.
+     */
+    public static final class DeclaredInSettingsPlugin implements Plugin<Project> {
+        @Override
+        public void apply(Project target) {}
+    }
+
     private void applyRepositories(RepositoryHandler repositories) {
         var mojangMaven = repositories.maven(repo -> {
             repo.setName("Mojang Minecraft Libraries");
diff --git a/src/test/java/net/neoforged/moddevgradle/functional/GroovyScriptTest.java b/src/test/java/net/neoforged/moddevgradle/functional/GroovyScriptTest.java
index 7ab4201f..02992c47 100644
--- a/src/test/java/net/neoforged/moddevgradle/functional/GroovyScriptTest.java
+++ b/src/test/java/net/neoforged/moddevgradle/functional/GroovyScriptTest.java
@@ -51,4 +51,34 @@ public void testApplyInEmptyProjectAndEnable() throws IOException {
         assertThat(result.getOutput()).contains("createMinecraftArtifacts");
         assertEquals(TaskOutcome.SUCCESS, result.task(":tasks").getOutcome());
     }
+
+    @Test
+    public void testApplyInSettings() throws IOException {
+        writeFile(settingsFile, """
+                plugins {
+                    id "net.neoforged.moddev.repositories"
+                }
+
+                rootProject.name = 'hello-world'
+
+                dependencyResolutionManagement {
+                    repositoriesMode = RepositoriesMode.FAIL_ON_PROJECT_REPOS
+                }
+                """);
+        String buildFileContent = """
+                plugins {
+                    id "net.neoforged.moddev"
+                }
+                """;
+        writeFile(buildFile, buildFileContent);
+
+        BuildResult result = GradleRunner.create()
+                .withPluginClasspath()
+                .withProjectDir(testProjectDir)
+                .withArguments("tasks", "--all", "-i")
+                .build();
+
+        assertThat(result.getOutput()).contains("Not enabling NeoForged repositories since they were applied at the settings level");
+        assertEquals(TaskOutcome.SUCCESS, result.task(":tasks").getOutcome());
+    }
 }