diff --git a/src/main/java/net/fabricmc/loom/configuration/ide/RunConfig.java b/src/main/java/net/fabricmc/loom/configuration/ide/RunConfig.java
index 78b472e..c25dc58 100644
--- a/src/main/java/net/fabricmc/loom/configuration/ide/RunConfig.java
+++ b/src/main/java/net/fabricmc/loom/configuration/ide/RunConfig.java
@@ -27,6 +27,7 @@ package net.fabricmc.loom.configuration.ide;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
 import java.util.Map;
 import java.util.Objects;
 
@@ -181,13 +182,23 @@ public class RunConfig {
 		return runConfig;
 	}
 
-	public String fromDummy(String dummy) throws IOException {
+	public String fromDummy(String dummy, boolean relativeDir, Project project) throws IOException {
 		String dummyConfig;
 
 		try (InputStream input = SetupIntelijRunConfigs.class.getClassLoader().getResourceAsStream(dummy)) {
 			dummyConfig = new String(input.readAllBytes(), StandardCharsets.UTF_8);
 		}
 
+		String runDir = this.runDir;
+
+		if (relativeDir && project.getRootProject() != project) {
+			Path rootPath = project.getRootDir().toPath();
+			Path projectPath = project.getProjectDir().toPath();
+			String relativePath = rootPath.relativize(projectPath).toString();
+
+			runDir = relativePath + "/" + runDir;
+		}
+
 		dummyConfig = dummyConfig.replace("%NAME%", configName);
 		dummyConfig = dummyConfig.replace("%MAIN_CLASS%", mainClass);
 		dummyConfig = dummyConfig.replace("%ECLIPSE_PROJECT%", eclipseProjectName);
diff --git a/src/main/java/net/fabricmc/loom/configuration/ide/RunConfigSettings.java b/src/main/java/net/fabricmc/loom/configuration/ide/RunConfigSettings.java
index 60548c2..a7a1c42 100644
--- a/src/main/java/net/fabricmc/loom/configuration/ide/RunConfigSettings.java
+++ b/src/main/java/net/fabricmc/loom/configuration/ide/RunConfigSettings.java
@@ -289,7 +289,7 @@ public final class RunConfigSettings implements Named {
 	}
 
 	public void makeRunDir() {
-		File file = new File(getProject().getRootDir(), runDir);
+		File file = new File(getProject().getProjectDir(), runDir);
 
 		if (!file.exists()) {
 			file.mkdir();
diff --git a/src/main/java/net/fabricmc/loom/configuration/ide/SetupIntelijRunConfigs.java b/src/main/java/net/fabricmc/loom/configuration/ide/SetupIntelijRunConfigs.java
index db815e9..8120a63 100644
--- a/src/main/java/net/fabricmc/loom/configuration/ide/SetupIntelijRunConfigs.java
+++ b/src/main/java/net/fabricmc/loom/configuration/ide/SetupIntelijRunConfigs.java
@@ -37,8 +37,6 @@ import net.fabricmc.loom.configuration.providers.minecraft.assets.MinecraftAsset
 
 public class SetupIntelijRunConfigs {
 	public static void setup(Project project) {
-		LoomGradleExtension extension = LoomGradleExtension.get(project);
-
 		File projectDir = project.getRootProject().file(".idea");
 
 		if (!projectDir.exists()) {
@@ -80,7 +78,7 @@ public class SetupIntelijRunConfigs {
 			String name = config.configName.replaceAll("[^a-zA-Z0-9$_]", "_");
 
 			File runConfigs = new File(runConfigsDir, name + projectPath + ".xml");
-			String runConfigXml = config.fromDummy("idea_run_config_template.xml");
+			String runConfigXml = config.fromDummy("idea_run_config_template.xml", true, project);
 
 			if (!runConfigs.exists()) {
 				FileUtils.writeStringToFile(runConfigs, runConfigXml, StandardCharsets.UTF_8);
diff --git a/src/main/java/net/fabricmc/loom/task/GenEclipseRunsTask.java b/src/main/java/net/fabricmc/loom/task/GenEclipseRunsTask.java
index acd2bc4..1e529bd 100644
--- a/src/main/java/net/fabricmc/loom/task/GenEclipseRunsTask.java
+++ b/src/main/java/net/fabricmc/loom/task/GenEclipseRunsTask.java
@@ -49,9 +49,9 @@ public class GenEclipseRunsTask extends AbstractLoomTask {
 
 			String name = settings.getName();
 
-			File configs = new File(getProject().getRootDir(), eclipseModel.getProject().getName() + "_" + name + ".launch");
+			File configs = new File(getProject().getProjectDir(), eclipseModel.getProject().getName() + "_" + name + ".launch");
 			RunConfig configInst = RunConfig.runConfig(getProject(), settings);
-			String config = configInst.fromDummy("eclipse_run_config_template.xml");
+			String config = configInst.fromDummy("eclipse_run_config_template.xml", false, getProject());
 
 			if (!configs.exists()) {
 				FileUtils.writeStringToFile(configs, config, StandardCharsets.UTF_8);
diff --git a/src/main/java/net/fabricmc/loom/task/GenVsCodeProjectTask.java b/src/main/java/net/fabricmc/loom/task/GenVsCodeProjectTask.java
index 287e1c0..2837cac 100644
--- a/src/main/java/net/fabricmc/loom/task/GenVsCodeProjectTask.java
+++ b/src/main/java/net/fabricmc/loom/task/GenVsCodeProjectTask.java
@@ -27,6 +27,7 @@ package net.fabricmc.loom.task;
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -78,7 +79,7 @@ public class GenVsCodeProjectTask extends AbstractLoomTask {
 		}
 	}
 
-	private static class VsCodeLaunch {
+	private class VsCodeLaunch {
 		public String version = "0.2.0";
 		public List<VsCodeConfiguration> configurations = new ArrayList<>();
 
@@ -88,7 +89,7 @@ public class GenVsCodeProjectTask extends AbstractLoomTask {
 	}
 
 	@SuppressWarnings("unused")
-	private static class VsCodeConfiguration {
+	private class VsCodeConfiguration {
 		public String type = "java";
 		public String name;
 		public String request = "launch";
@@ -105,6 +106,14 @@ public class GenVsCodeProjectTask extends AbstractLoomTask {
 			this.vmArgs = runConfig.vmArgs;
 			this.args = runConfig.programArgs;
 			this.cwd = "${workspaceFolder}/" + runConfig.runDir;
+
+			if (getProject().getRootProject() != getProject()) {
+				Path rootPath = getProject().getRootDir().toPath();
+				Path projectPath = getProject().getProjectDir().toPath();
+				String relativePath = rootPath.relativize(projectPath).toString();
+
+				this.cwd = "${workspaceFolder}/%s/%s".formatted(relativePath, runConfig.runDir);
+			}
 		}
 	}
 }
diff --git a/src/test/groovy/net/fabricmc/loom/test/integration/MultiProjectTest.groovy b/src/test/groovy/net/fabricmc/loom/test/integration/MultiProjectTest.groovy
index 11de0ef..5aa5b70 100644
--- a/src/test/groovy/net/fabricmc/loom/test/integration/MultiProjectTest.groovy
+++ b/src/test/groovy/net/fabricmc/loom/test/integration/MultiProjectTest.groovy
@@ -38,7 +38,7 @@ class MultiProjectTest extends Specification implements GradleProjectTestTrait {
 			def gradle = gradleProject(project: "multiproject", version: version)
 
 		when:
-			def result = gradle.run(task: "build")
+			def result = gradle.run(tasks: ["build", "eclipse", "vscode", "idea"])
 
 		then:
 			result.task(":build").outcome == SUCCESS
diff --git a/src/test/resources/projects/multiproject/example/build.gradle b/src/test/resources/projects/multiproject/example/build.gradle
index c40184a..65ab979 100644
--- a/src/test/resources/projects/multiproject/example/build.gradle
+++ b/src/test/resources/projects/multiproject/example/build.gradle
@@ -2,4 +2,10 @@ archivesBaseName = "example"
 
 dependencies {
 	implementation project(path: ":core", configuration: "dev")
+}
+
+loom {
+	runConfigs.configureEach {
+		ideConfigGenerated = true
+	}
 }
\ No newline at end of file