diff --git a/src/config/config-resolver.test.ts b/src/config/config-resolver.test.ts
index e6d0ff773..05acf6ece 100644
--- a/src/config/config-resolver.test.ts
+++ b/src/config/config-resolver.test.ts
@@ -226,6 +226,32 @@ describe("config-resolver", () => {
       expect(config.getOutputRoots()).toContain(resolve("./app2"));
       expect(config.getOutputRoots()).toContain(resolve("./app3"));
     });
+
+    it("should resolve outputRoots configured per target", async () => {
+      const configContent = JSON.stringify({
+        targets: ["copilot", "claudecode"],
+        outputRoots: {
+          copilot: "./build/copilot",
+          claudecode: ["./build/claudecode", "./build/claude-extra"],
+        },
+      });
+      await writeFileContent(join(testDir, "rulesync.jsonc"), configContent);
+
+      const config = await ConfigResolver.resolve({
+        configPath: join(testDir, "rulesync.jsonc"),
+      });
+
+      expect(config.getOutputRoots("copilot")).toEqual([resolve("./build/copilot")]);
+      expect(config.getOutputRoots("claudecode")).toEqual([
+        resolve("./build/claudecode"),
+        resolve("./build/claude-extra"),
+      ]);
+      expect(config.getOutputRoots()).toEqual([
+        resolve("./build/copilot"),
+        resolve("./build/claudecode"),
+        resolve("./build/claude-extra"),
+      ]);
+    });
   });
 
   describe("local configuration (rulesync.local.jsonc)", () => {
diff --git a/src/config/config-resolver.ts b/src/config/config-resolver.ts
index ef2f413eb..3ec122b1d 100644
--- a/src/config/config-resolver.ts
+++ b/src/config/config-resolver.ts
@@ -30,6 +30,7 @@ import {
   PartialConfigParams,
   RequiredConfigParams,
 } from "./config.js";
+import type { OutputRoots } from "./config.js";
 
 /**
  * CLI-resolvable params exclude `sources` — sources are config-file-only.
@@ -372,9 +373,9 @@ function getOutputRootsInLightOfGlobal({
   outputRoots,
   global,
 }: {
-  outputRoots: string[];
+  outputRoots: OutputRoots;
   global: boolean;
-}): string[] {
+}): OutputRoots {
   if (global) {
     // When global is true, the base directory is always the home directory
     return [getHomeDirectory()];
@@ -383,11 +384,26 @@ function getOutputRootsInLightOfGlobal({
   // Validate the *raw* user input first so traversal patterns like
   // `/foo/../bar` cannot slip through `resolve()`'s normalization. Then
   // resolve to absolute for downstream consumers.
-  outputRoots.forEach((outputRoot) => {
-    validateOutputRoot(outputRoot);
-  });
+  if (Array.isArray(outputRoots)) {
+    outputRoots.forEach((outputRoot) => {
+      validateOutputRoot(outputRoot);
+    });
+
+    return outputRoots.map((outputRoot) => resolve(outputRoot));
+  }
+
+  const resolvedOutputRoots: OutputRoots = {};
+  for (const [target, targetOutputRoots] of Object.entries(outputRoots)) {
+    const roots = Array.isArray(targetOutputRoots) ? targetOutputRoots : [targetOutputRoots];
+    roots.forEach((outputRoot) => {
+      validateOutputRoot(outputRoot);
+    });
+    resolvedOutputRoots[target as ToolTarget] = Array.isArray(targetOutputRoots)
+      ? roots.map((outputRoot) => resolve(outputRoot))
+      : resolve(targetOutputRoots);
+  }
 
-  return outputRoots.map((outputRoot) => resolve(outputRoot));
+  return resolvedOutputRoots;
 }
 
 function extractConfigFileTargets(
diff --git a/src/config/config.ts b/src/config/config.ts
index 17a4dc225..415e9aa50 100644
--- a/src/config/config.ts
+++ b/src/config/config.ts
@@ -58,8 +58,11 @@ const SourceEntrySchema = z.object({
 });
 export type SourceEntry = z.infer<typeof SourceEntrySchema>;
 
-const ConfigParamsSchema = z.object({
-  outputRoots: z.array(z.string()),
+export const ConfigParamsSchema = z.object({
+  outputRoots: z.union([
+    z.array(z.string()),
+    z.record(z.string(), z.union([z.string(), z.array(z.string())])),
+  ]),
   targets: RulesyncConfigTargetsSchema,
   features: RulesyncFeaturesSchema,
   verbose: z.boolean(),
@@ -99,7 +102,9 @@ const ConfigParamsSchema = z.object({
 // `assertTargetsOrFeaturesProvided`. Programmatic callers constructing
 // `Config` directly must respect these invariants.
 type InferredConfigParams = z.infer<typeof ConfigParamsSchema>;
+export type OutputRoots = string[] | Partial<Record<ToolTarget, string | string[]>>;
 export type ConfigParams = Omit<InferredConfigParams, "targets" | "features"> & {
+  outputRoots: OutputRoots;
   targets?: RulesyncConfigTargets;
   features?: RulesyncFeatures;
   configFileTargets?: ToolTarget[];
@@ -108,6 +113,7 @@ export type ConfigParams = Omit<InferredConfigParams, "targets" | "features"> &
 const PartialConfigParamsSchema = z.partial(ConfigParamsSchema);
 type InferredPartialConfigParams = z.infer<typeof PartialConfigParamsSchema>;
 export type PartialConfigParams = Omit<InferredPartialConfigParams, "targets" | "features"> & {
+  outputRoots?: OutputRoots;
   targets?: RulesyncConfigTargets;
   features?: RulesyncFeatures;
 };
@@ -119,6 +125,7 @@ export const ConfigFileSchema = z.object({
 });
 type InferredConfigFile = z.infer<typeof ConfigFileSchema>;
 export type ConfigFile = Omit<InferredConfigFile, "targets" | "features"> & {
+  outputRoots?: OutputRoots;
   targets?: RulesyncConfigTargets;
   features?: RulesyncFeatures;
 };
@@ -126,6 +133,7 @@ export type ConfigFile = Omit<InferredConfigFile, "targets" | "features"> & {
 const RequiredConfigParamsSchema = z.required(ConfigParamsSchema);
 type InferredRequiredConfigParams = z.infer<typeof RequiredConfigParamsSchema>;
 export type RequiredConfigParams = Omit<InferredRequiredConfigParams, "targets" | "features"> & {
+  outputRoots: OutputRoots;
   targets?: RulesyncConfigTargets;
   features?: RulesyncFeatures;
 };
@@ -207,7 +215,7 @@ const assertTargetsOrFeaturesProvided = ({
 };
 
 export class Config {
-  private readonly outputRoots: string[];
+  private readonly outputRoots: OutputRoots;
   private readonly targets: RulesyncConfigTargets;
   private readonly features: RulesyncFeatures;
   /**
@@ -274,6 +282,7 @@ export class Config {
     // Reject unknown keys in the object form of `targets`. Array-form values
     // are already validated at the Zod schema level.
     this.validateObjectFormTargetKeys(resolvedTargets);
+    this.validateObjectFormOutputRootKeys(outputRoots);
 
     // Validate conflicting targets (accepts array and object forms)
     this.validateConflictingTargets(resolvedTargets);
@@ -346,6 +355,18 @@ export class Config {
     }
   }
 
+  private validateObjectFormOutputRootKeys(outputRoots: OutputRoots): void {
+    if (Array.isArray(outputRoots)) return;
+    const validTargets = new Set<string>(ALL_TOOL_TARGETS);
+    for (const key of Object.keys(outputRoots)) {
+      if (!validTargets.has(key)) {
+        throw new Error(
+          `Unknown outputRoots target '${key}'. Valid targets: ${ALL_TOOL_TARGETS.join(", ")}.`,
+        );
+      }
+    }
+  }
+
   private validateConflictingTargets(targets: RulesyncConfigTargets): void {
     // Wildcard (*) doesn't include legacy targets, so conflicts can only
     // occur when both sides of a conflicting pair are explicitly present.
@@ -366,8 +387,25 @@ export class Config {
     }
   }
 
-  public getOutputRoots(): string[] {
-    return this.outputRoots;
+  public getOutputRoots(): string[];
+  public getOutputRoots(target: ToolTarget): string[];
+  public getOutputRoots(target?: ToolTarget): string[] {
+    if (Array.isArray(this.outputRoots)) {
+      return this.outputRoots;
+    }
+
+    if (target) {
+      const targetOutputRoots = this.outputRoots[target];
+      if (targetOutputRoots === undefined) return [];
+      return Array.isArray(targetOutputRoots) ? targetOutputRoots : [targetOutputRoots];
+    }
+
+    const allRoots: string[] = [];
+    for (const value of Object.values(this.outputRoots)) {
+      if (value === undefined) continue;
+      allRoots.push(...(Array.isArray(value) ? value : [value]));
+    }
+    return [...new Set(allRoots)];
   }
 
   /**
diff --git a/src/lib/generate.ts b/src/lib/generate.ts
index 72100c41f..1b0a8fb29 100644
--- a/src/lib/generate.ts
+++ b/src/lib/generate.ts
@@ -490,8 +490,8 @@ async function generateRulesCore(params: {
       })
     : new Map<string, ToolTarget>();
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if rules feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("rules")) {
         continue;
@@ -566,7 +566,7 @@ async function generateIgnoreCore(params: {
       continue;
     }
 
-    for (const outputRoot of config.getOutputRoots()) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       try {
         const processor = new IgnoreProcessor({
           // Pass `outputRoot` verbatim. The legacy
@@ -619,8 +619,8 @@ async function generateMcpCore(params: {
     logger,
   });
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if mcp feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("mcp")) {
         continue;
@@ -670,8 +670,8 @@ async function generateCommandsCore(params: {
     logger,
   });
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if commands feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("commands")) {
         continue;
@@ -726,8 +726,8 @@ async function generateSubagentsCore(params: {
     logger,
   });
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if subagents feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("subagents")) {
         continue;
@@ -778,8 +778,8 @@ async function generateSkillsCore(params: {
     logger,
   });
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if skills feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("skills")) {
         continue;
@@ -838,8 +838,8 @@ async function generateHooksCore(params: {
     logger,
   });
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of toolTargets) {
+  for (const toolTarget of toolTargets) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       // Check if hooks feature is enabled for this specific target
       if (!config.getFeatures(toolTarget).includes("hooks")) {
         continue;
@@ -886,8 +886,8 @@ async function generatePermissionsCore(params: {
   const allPaths: string[] = [];
   let hasDiff = false;
 
-  for (const outputRoot of config.getOutputRoots()) {
-    for (const toolTarget of intersection(config.getTargets(), supportedPermissionsTargets)) {
+  for (const toolTarget of intersection(config.getTargets(), supportedPermissionsTargets)) {
+    for (const outputRoot of config.getOutputRoots(toolTarget)) {
       if (!config.getFeatures(toolTarget).includes("permissions")) {
         continue;
       }