diff --git a/apps/cli/src/commands/credentials.ts b/apps/cli/src/commands/credentials.ts
index 68ca2785..d14f6cdf 100644
--- a/apps/cli/src/commands/credentials.ts
+++ b/apps/cli/src/commands/credentials.ts
@@ -9,7 +9,7 @@
 
 import { existsSync, mkdirSync, writeFileSync, chmodSync } from "node:fs";
 import { dirname } from "node:path";
-import { getCredentialsPath, getSkillsEnvPath } from "@multica/core";
+import { getCredentialsPath } from "@multica/core";
 import { cyan, yellow, green, dim, red } from "../colors.js";
 
 type Command = "init" | "show" | "edit" | "help";
@@ -17,10 +17,7 @@ type Command = "init" | "show" | "edit" | "help";
 interface CredentialsOptions {
   command: Command;
   force: boolean;
-  coreOnly: boolean;
-  skillsOnly: boolean;
   pathOverride?: string | undefined;
-  skillsPathOverride?: string | undefined;
 }
 
 function printHelp() {
@@ -28,21 +25,20 @@ function printHelp() {
 ${cyan("Usage:")} multica credentials <command> [options]
 
 ${cyan("Commands:")}
-  ${yellow("init")}                Create credentials.json5 and skills.env.json5
+  ${yellow("init")}                Create credentials.json5
   ${yellow("show")}                Show credential file paths
   ${yellow("edit")}                Open credentials directory in file manager
   ${yellow("help")}                Show this help
 
 ${cyan("Options for 'init':")}
   ${yellow("--force")}             Overwrite existing files
-  ${yellow("--core-only")}         Only create credentials.json5
-  ${yellow("--skills-only")}       Only create skills.env.json5
   ${yellow("--path")} PATH         Override credentials path
-  ${yellow("--skills-path")} PATH  Override skills env path
 
 ${cyan("Files Created:")}
   ~/.super-multica/credentials.json5     LLM providers + tools config
-  ~/.super-multica/skills.env.json5      Skills/plugins/integrations env vars
+
+${dim("Skill-specific API keys are stored in .env files within each skill's directory.")}
+${dim("Example: ~/.super-multica/skills/<skill-id>/.env")}
 
 ${cyan("Examples:")}
   ${dim("# Initialize credentials")}
@@ -50,9 +46,6 @@ ${cyan("Examples:")}
 
   ${dim("# Force overwrite")}
   multica credentials init --force
-
-  ${dim("# Only create core credentials")}
-  multica credentials init --core-only
 `);
 }
 
@@ -61,8 +54,6 @@ function parseArgs(argv: string[]): CredentialsOptions {
   const opts: CredentialsOptions = {
     command: "help",
     force: false,
-    coreOnly: false,
-    skillsOnly: false,
   };
 
   const positional: string[] = [];
@@ -79,22 +70,10 @@ function parseArgs(argv: string[]): CredentialsOptions {
       opts.force = true;
       continue;
     }
-    if (arg === "--core-only") {
-      opts.coreOnly = true;
-      continue;
-    }
-    if (arg === "--skills-only") {
-      opts.skillsOnly = true;
-      continue;
-    }
     if (arg === "--path") {
       opts.pathOverride = args.shift();
       continue;
     }
-    if (arg === "--skills-path") {
-      opts.skillsPathOverride = args.shift();
-      continue;
-    }
     positional.push(arg);
   }
 
@@ -119,58 +98,25 @@ function buildCoreTemplate(): string {
 `;
 }
 
-function buildSkillsTemplate(): string {
-  return `{
-  env: {
-    // Dynamic keys (skills, plugins, integrations)
-    // LINEAR_API_KEY: "lin-..."
-  }
-}
-`;
-}
-
 function cmdInit(opts: CredentialsOptions): void {
-  const createCore = !opts.skillsOnly;
-  const createSkills = !opts.coreOnly;
-
-  if (!createCore && !createSkills) {
-    console.error(`${red("Error:")} Both --core-only and --skills-only were provided.`);
+  const path = opts.pathOverride ?? getCredentialsPath();
+  if (existsSync(path) && !opts.force) {
+    console.error(`${red("Error:")} Credentials file already exists at ${path}`);
+    console.error("Use --force to overwrite.");
     process.exit(1);
   }
-
-  if (createCore) {
-    const path = opts.pathOverride ?? getCredentialsPath();
-    if (existsSync(path) && !opts.force) {
-      console.error(`${red("Error:")} Credentials file already exists at ${path}`);
-      console.error("Use --force to overwrite.");
-      process.exit(1);
-    }
-    mkdirSync(dirname(path), { recursive: true });
-    writeFileSync(path, buildCoreTemplate(), "utf8");
-    chmodSync(path, 0o600);
-    console.log(`${green("Created:")} ${path}`);
-  }
-
-  if (createSkills) {
-    const skillsPath = opts.skillsPathOverride ?? getSkillsEnvPath();
-    if (existsSync(skillsPath) && !opts.force) {
-      console.error(`${red("Error:")} Skills env file already exists at ${skillsPath}`);
-      console.error("Use --force to overwrite.");
-      process.exit(1);
-    }
-    mkdirSync(dirname(skillsPath), { recursive: true });
-    writeFileSync(skillsPath, buildSkillsTemplate(), "utf8");
-    chmodSync(skillsPath, 0o600);
-    console.log(`${green("Created:")} ${skillsPath}`);
-  }
+  mkdirSync(dirname(path), { recursive: true });
+  writeFileSync(path, buildCoreTemplate(), "utf8");
+  chmodSync(path, 0o600);
+  console.log(`${green("Created:")} ${path}`);
 
   console.log("");
-  console.log("Edit these files to add your credentials.");
+  console.log("Edit this file to add your LLM provider credentials.");
+  console.log(`${dim("Skill-specific API keys go in .env files within each skill's directory.")}`);
 }
 
 function cmdShow(): void {
   const credentialsPath = getCredentialsPath();
-  const skillsEnvPath = getSkillsEnvPath();
 
   console.log(`\n${cyan("Credential Files:")}\n`);
 
@@ -179,12 +125,10 @@ function cmdShow(): void {
   console.log(`  Exists: ${existsSync(credentialsPath) ? green("Yes") : red("No")}`);
   console.log("");
 
-  console.log(`${yellow("skills.env.json5")}`);
-  console.log(`  Path: ${skillsEnvPath}`);
-  console.log(`  Exists: ${existsSync(skillsEnvPath) ? green("Yes") : red("No")}`);
+  console.log(`${dim("Skill-specific API keys are stored in .env files within each skill's directory.")}`);
   console.log("");
 
-  if (!existsSync(credentialsPath) || !existsSync(skillsEnvPath)) {
+  if (!existsSync(credentialsPath)) {
     console.log(`${dim("Run 'multica credentials init' to create missing files.")}`);
   }
 }
diff --git a/apps/cli/src/commands/skills.ts b/apps/cli/src/commands/skills.ts
index d9bf5e20..a6971fa0 100644
--- a/apps/cli/src/commands/skills.ts
+++ b/apps/cli/src/commands/skills.ts
@@ -19,7 +19,6 @@ import {
   checkEligibilityDetailed,
   type DiagnosticItem,
 } from "@multica/core";
-import { credentialManager } from "@multica/core";
 import { cyan, yellow, green, dim, red } from "../colors.js";
 
 type Command = "list" | "status" | "install" | "add" | "remove" | "help";
@@ -268,7 +267,7 @@ function cmdStatusDetail(manager: SkillManager, skillId: string, verbose?: boole
 
     if (hasEnvs > 0) {
       const envs = requirements?.env ?? metadata?.requiresEnv ?? [];
-      printRequirementStatus("Environment vars", envs, checkEnvVars);
+      printRequirementStatus("Environment vars", envs, (e) => checkEnvVars(e, skill.env));
     }
   }
 
@@ -360,10 +359,11 @@ function checkBinaries(bins: string[]): Map<string, boolean> {
   return result;
 }
 
-function checkEnvVars(envs: string[]): Map<string, boolean> {
+function checkEnvVars(envs: string[], skillEnv: Record<string, string>): Map<string, boolean> {
   const result = new Map<string, boolean>();
   for (const env of envs) {
-    result.set(env, credentialManager.hasEnv(env));
+    const found = Object.prototype.hasOwnProperty.call(skillEnv, env) || env in process.env;
+    result.set(env, found);
   }
   return result;
 }
diff --git a/apps/cli/src/skills.ts b/apps/cli/src/skills.ts
index 64169ca4..4eca4601 100644
--- a/apps/cli/src/skills.ts
+++ b/apps/cli/src/skills.ts
@@ -22,7 +22,6 @@ import {
   checkEligibilityDetailed,
   type DiagnosticItem,
 } from "@multica/core";
-import { credentialManager } from "@multica/core";
 
 // ============================================================================
 // Types
@@ -268,7 +267,7 @@ function cmdStatusDetail(manager: SkillManager, skillId: string, verbose?: boole
 
     if (hasEnvs > 0) {
       const envs = requirements?.env ?? metadata?.requiresEnv ?? [];
-      printRequirementStatus("Environment vars", envs, checkEnvVars);
+      printRequirementStatus("Environment vars", envs, (e) => checkEnvVars(e, skill.env));
     }
   }
 
@@ -363,10 +362,11 @@ function checkBinaries(bins: string[]): Map<string, boolean> {
   return result;
 }
 
-function checkEnvVars(envs: string[]): Map<string, boolean> {
+function checkEnvVars(envs: string[], skillEnv: Record<string, string>): Map<string, boolean> {
   const result = new Map<string, boolean>();
   for (const env of envs) {
-    result.set(env, credentialManager.hasEnv(env));
+    const found = Object.prototype.hasOwnProperty.call(skillEnv, env) || env in process.env;
+    result.set(env, found);
   }
   return result;
 }
diff --git a/packages/core/src/agent/credentials-cli.ts b/packages/core/src/agent/credentials-cli.ts
index d5fa9a13..316c3e69 100644
--- a/packages/core/src/agent/credentials-cli.ts
+++ b/packages/core/src/agent/credentials-cli.ts
@@ -3,12 +3,12 @@
  * Credentials CLI
  *
  * Commands:
- *   init       Create credentials.json5 and skills.env.json5
+ *   init       Create credentials.json5
  */
 
 import { existsSync, mkdirSync, writeFileSync, chmodSync } from "node:fs";
 import { dirname } from "node:path";
-import { getCredentialsPath, getSkillsEnvPath } from "./credentials.js";
+import { getCredentialsPath } from "./credentials.js";
 
 type Command = "init" | "help";
 
@@ -16,21 +16,19 @@ function printUsage(): void {
   console.log("Usage: pnpm credentials:cli <command> [options]");
   console.log("");
   console.log("Commands:");
-  console.log("  init        Create credentials.json5 and skills.env.json5 (empty templates)");
+  console.log("  init        Create credentials.json5 (empty template)");
   console.log("  help        Show this help");
   console.log("");
   console.log("Options:");
   console.log("  --force         Overwrite existing files");
-  console.log("  --core-only     Only create credentials.json5");
-  console.log("  --skills-only   Only create skills.env.json5");
   console.log("  --path          Override credentials path (SMC_CREDENTIALS_PATH)");
-  console.log("  --skills-path   Override skills env path (SMC_SKILLS_ENV_PATH)");
+  console.log("");
+  console.log("Skill-specific API keys are stored in .env files within each skill's directory.");
+  console.log("Example: ~/.super-multica/skills/<skill-id>/.env");
   console.log("");
   console.log("Examples:");
   console.log("  pnpm credentials:cli init");
   console.log("  pnpm credentials:cli init --force");
-  console.log("  pnpm credentials:cli init --core-only");
-  console.log("  pnpm credentials:cli init --skills-only");
 }
 
 function buildCoreTemplate(): string {
@@ -51,23 +49,10 @@ function buildCoreTemplate(): string {
 `;
 }
 
-function buildSkillsTemplate(): string {
-  return `{
-  env: {
-    // Dynamic keys (skills, plugins, integrations)
-    // LINEAR_API_KEY: "lin-..."
-  }
-}
-`;
-}
-
 function parseArgs(argv: string[]) {
   const args = [...argv];
   let force = false;
   let pathOverride: string | undefined;
-  let skillsPathOverride: string | undefined;
-  let coreOnly = false;
-  let skillsOnly = false;
   const positional: string[] = [];
 
   while (args.length > 0) {
@@ -77,76 +62,42 @@ function parseArgs(argv: string[]) {
       force = true;
       continue;
     }
-    if (arg === "--core-only") {
-      coreOnly = true;
-      continue;
-    }
-    if (arg === "--skills-only") {
-      skillsOnly = true;
-      continue;
-    }
     if (arg === "--path") {
       pathOverride = args.shift();
       continue;
     }
-    if (arg === "--skills-path") {
-      skillsPathOverride = args.shift();
-      continue;
-    }
     if (arg === "--help" || arg === "-h") {
-      return { command: "help" as Command, force, pathOverride, skillsPathOverride, coreOnly, skillsOnly };
+      return { command: "help" as Command, force, pathOverride };
     }
     positional.push(arg);
   }
 
   const command = (positional[0] || "help") as Command;
-  return { command, force, pathOverride, skillsPathOverride, coreOnly, skillsOnly };
+  return { command, force, pathOverride };
 }
 
-function cmdInit(force: boolean, pathOverride?: string, skillsPathOverride?: string, coreOnly?: boolean, skillsOnly?: boolean): void {
-  const createCore = skillsOnly ? false : true;
-  const createSkills = coreOnly ? false : true;
-
-  if (!createCore && !createSkills) {
-    console.error("Error: both --core-only and --skills-only were provided.");
+function cmdInit(force: boolean, pathOverride?: string): void {
+  const path = pathOverride ?? getCredentialsPath();
+  if (existsSync(path) && !force) {
+    console.error(`Error: credentials file already exists at ${path}`);
+    console.error("Use --force to overwrite.");
     process.exit(1);
   }
+  mkdirSync(dirname(path), { recursive: true });
+  writeFileSync(path, buildCoreTemplate(), "utf8");
+  chmodSync(path, 0o600);
+  console.log(`Created: ${path}`);
 
-  if (createCore) {
-    const path = pathOverride ?? getCredentialsPath();
-    if (existsSync(path) && !force) {
-      console.error(`Error: credentials file already exists at ${path}`);
-      console.error("Use --force to overwrite.");
-      process.exit(1);
-    }
-    mkdirSync(dirname(path), { recursive: true });
-    writeFileSync(path, buildCoreTemplate(), "utf8");
-    chmodSync(path, 0o600);
-    console.log(`Created: ${path}`);
-  }
-
-  if (createSkills) {
-    const skillsPath = skillsPathOverride ?? getSkillsEnvPath();
-    if (existsSync(skillsPath) && !force) {
-      console.error(`Error: skills env file already exists at ${skillsPath}`);
-      console.error("Use --force to overwrite.");
-      process.exit(1);
-    }
-    mkdirSync(dirname(skillsPath), { recursive: true });
-    writeFileSync(skillsPath, buildSkillsTemplate(), "utf8");
-    chmodSync(skillsPath, 0o600);
-    console.log(`Created: ${skillsPath}`);
-  }
-
-  console.log("Edit these files to add your credentials.");
+  console.log("Edit this file to add your credentials.");
+  console.log("Skill-specific API keys go in .env files within each skill's directory.");
 }
 
 async function main() {
-  const { command, force, pathOverride, skillsPathOverride, coreOnly, skillsOnly } = parseArgs(process.argv.slice(2));
+  const { command, force, pathOverride } = parseArgs(process.argv.slice(2));
 
   switch (command) {
     case "init":
-      cmdInit(force, pathOverride, skillsPathOverride, coreOnly, skillsOnly);
+      cmdInit(force, pathOverride);
       break;
     case "help":
     default:
diff --git a/packages/core/src/agent/credentials.ts b/packages/core/src/agent/credentials.ts
index edc501ea..6e6f8363 100644
--- a/packages/core/src/agent/credentials.ts
+++ b/packages/core/src/agent/credentials.ts
@@ -35,12 +35,7 @@ export type CredentialsConfig = {
   channels?: Record<string, Record<string, Record<string, unknown>> | undefined> | undefined;
 };
 
-type SkillsEnvConfig = {
-  env?: Record<string, string> | undefined;
-};
-
 const DEFAULT_CREDENTIALS_PATH = join(DATA_DIR, "credentials.json5");
-const DEFAULT_SKILLS_ENV_PATH = join(DATA_DIR, "skills.env.json5");
 
 function expandHome(value: string): string {
   if (value === "~") return homedir();
@@ -58,42 +53,16 @@ function isTestEnv(): boolean {
   );
 }
 
-function isString(value: unknown): value is string {
-  return typeof value === "string";
-}
-
-function setEnvValue(target: Record<string, string>, key: string, value: unknown): void {
-  if (isString(value)) {
-    target[key] = value;
-  }
-}
-
-function applyEnvMap(target: Record<string, string>, env?: Record<string, string>): void {
-  if (!env) return;
-  for (const [key, value] of Object.entries(env)) {
-    setEnvValue(target, key, value);
-  }
-}
-
 export function getCredentialsPath(): string {
   const raw = process.env.SMC_CREDENTIALS_PATH ?? DEFAULT_CREDENTIALS_PATH;
   return expandHome(raw);
 }
 
-export function getSkillsEnvPath(): string {
-  const raw = process.env.SMC_SKILLS_ENV_PATH ?? DEFAULT_SKILLS_ENV_PATH;
-  return expandHome(raw);
-}
-
 export class CredentialManager {
   private corePath: string | null = null;
-  private skillsPath: string | null = null;
   private disabledState: boolean | null = null;
   private coreConfig: CredentialsConfig | null = null;
-  private skillsConfig: SkillsEnvConfig | null = null;
-  private resolvedSkillsEnv: Record<string, string> | null = null;
   private coreMtimeMs: number | null = null;
-  private skillsMtimeMs: number | null = null;
 
   private isDisabled(): boolean {
     if (process.env.SMC_CREDENTIALS_DISABLE === "1") return true;
@@ -139,63 +108,6 @@ export class CredentialManager {
     }
   }
 
-  private loadSkillsEnv(): void {
-    const path = getSkillsEnvPath();
-    const disabled = this.isDisabled();
-    let mtimeMs: number | null = null;
-
-    if (!disabled && existsSync(path)) {
-      try {
-        mtimeMs = statSync(path).mtimeMs;
-      } catch {
-        mtimeMs = null;
-      }
-    }
-
-    if (
-      this.skillsPath === path
-      && this.disabledState === disabled
-      && this.resolvedSkillsEnv
-      && this.skillsMtimeMs === mtimeMs
-    ) {
-      return;
-    }
-
-    this.skillsPath = path;
-    this.disabledState = disabled;
-    this.skillsConfig = null;
-    this.resolvedSkillsEnv = null;
-    this.skillsMtimeMs = mtimeMs;
-
-    if (disabled) return;
-    if (mtimeMs === null) return;
-
-    const raw = readFileSync(path, "utf8");
-    try {
-      this.skillsConfig = JSON5.parse(raw) as SkillsEnvConfig;
-    } catch (err) {
-      const message = err instanceof Error ? err.message : String(err);
-      throw new Error(`Failed to parse skills env file (${path}): ${message}`);
-    }
-  }
-
-  private buildSkillsEnv(): Record<string, string> {
-    const env: Record<string, string> = {};
-    if (!this.skillsConfig) return env;
-
-    applyEnvMap(env, this.skillsConfig.env);
-
-    return env;
-  }
-
-  private getResolvedSkillsEnv(): Record<string, string> {
-    this.loadSkillsEnv();
-    if (!this.resolvedSkillsEnv) {
-      this.resolvedSkillsEnv = this.buildSkillsEnv();
-    }
-    return this.resolvedSkillsEnv;
-  }
-
   getLlmProvider(): string | undefined {
     this.loadCore();
     return this.coreConfig?.llm?.provider;
@@ -211,22 +123,6 @@ export class CredentialManager {
     return this.coreConfig?.tools?.[toolName];
   }
 
-  getEnv(name: string): string | undefined {
-    const resolved = this.getResolvedSkillsEnv();
-    if (Object.prototype.hasOwnProperty.call(resolved, name)) {
-      return resolved[name];
-    }
-    return process.env[name];
-  }
-
-  hasEnv(name: string): boolean {
-    const resolved = this.getResolvedSkillsEnv();
-    if (Object.prototype.hasOwnProperty.call(resolved, name)) {
-      return true;
-    }
-    return name in process.env;
-  }
-
   /**
    * Get explicit profile order for a provider from credentials.json5 `llm.order`.
    * Returns undefined if no explicit order is configured.
@@ -257,19 +153,11 @@ export class CredentialManager {
     return this.coreConfig?.channels ?? {};
   }
 
-  getResolvedEnvSnapshot(): Record<string, string> {
-    return { ...this.getResolvedSkillsEnv() };
-  }
-
   reset(): void {
     this.corePath = null;
-    this.skillsPath = null;
     this.disabledState = null;
     this.coreConfig = null;
-    this.skillsConfig = null;
-    this.resolvedSkillsEnv = null;
     this.coreMtimeMs = null;
-    this.skillsMtimeMs = null;
   }
 
   /**
diff --git a/packages/core/src/agent/index.ts b/packages/core/src/agent/index.ts
index 13325fe0..6dccd6f7 100644
--- a/packages/core/src/agent/index.ts
+++ b/packages/core/src/agent/index.ts
@@ -7,7 +7,7 @@ export * from "./skills/index.js";
 export * from "./channel.js";
 export * from "./sync-agent.js";
 export * from "./async-agent.js";
-export { credentialManager, getCredentialsPath, getSkillsEnvPath, type CredentialsConfig } from "./credentials.js";
+export { credentialManager, getCredentialsPath, type CredentialsConfig } from "./credentials.js";
 export * from "./providers/index.js";
 export * from "./tools.js";
 export * from "./tools/policy.js";