diff --git a/packages/cli/src/commands/build/build.schema.ts b/packages/cli/src/commands/build/build.schema.ts
index c5063d9..9643052 100644
--- a/packages/cli/src/commands/build/build.schema.ts
+++ b/packages/cli/src/commands/build/build.schema.ts
@@ -1,22 +1,24 @@
 import z from "zod";
 
 export const buildConfigSchema = z.object({
-  manifest: z.object({
-    prefix: z
-      .string()
-      .describe("Default prefix for documentation links")
-      .default("docs/references"),
-    enabled: z
-      .boolean()
-      .describe("Whether to generate manifest.json file")
-      .default(true),
-    path: z
-      .string()
-      .describe(
-        "Path to save manifest file (relative to project root or absolute path). If not specified, uses outputDir/manifest.json",
-      )
-      .optional(),
-  }),
+  manifest: z
+    .object({
+      prefix: z
+        .string()
+        .describe("Default prefix for documentation links")
+        .default("docs/references"),
+      enabled: z
+        .boolean()
+        .describe("Whether to generate manifest.json file")
+        .default(true),
+      path: z
+        .string()
+        .describe(
+          "Path to save manifest file (relative to project root or absolute path). If not specified, uses outputDir/manifest.json",
+        )
+        .optional(),
+    })
+    .default({}),
   outputDir: z
     .string()
     .describe("Directory where build output will be saved")
diff --git a/packages/cli/src/commands/check/check.schema.ts b/packages/cli/src/commands/check/check.schema.ts
index 9ae2da7..35fa9c5 100644
--- a/packages/cli/src/commands/check/check.schema.ts
+++ b/packages/cli/src/commands/check/check.schema.ts
@@ -1,5 +1,7 @@
 import { z } from "zod";
 
-export const checkConfigSchema = z.object({
-  entryPoints: z.array(z.string()).optional().describe("Entry points to check"),
-});
+export const checkConfigSchema = z
+	.object({
+  	entryPoints: z.array(z.string()).optional().describe("Entry points to check"),
+	})
+	.default({});
diff --git a/packages/cli/src/config/config.schema.ts b/packages/cli/src/config/config.schema.ts
index a2427ab..d0f169b 100644
--- a/packages/cli/src/config/config.schema.ts
+++ b/packages/cli/src/config/config.schema.ts
@@ -13,7 +13,8 @@ export const configSchema = z.object({
         .describe("Package patterns to include in build"),
       exclude: z
         .array(z.string())
-        .describe("Package patterns to exclude from build"),
+        .describe("Package patterns to exclude from build")
+        .default([]),
     }),
   }),
   commands: z.object({
@@ -58,4 +59,6 @@ export const configSchema = z.object({
  * @param {function} plugins.plugin Factory function that returns plugin instance
  * @param {object} [plugins.options] Plugin options
  */
-export type Config = z.infer<typeof configSchema>;
+export type Config = z.input<typeof configSchema>;
+
+export type ResolvedConfig = z.output<typeof configSchema>;
diff --git a/packages/cli/src/plugins/load-plugins.ts b/packages/cli/src/plugins/load-plugins.ts
index b5c3a99..edf27c1 100644
--- a/packages/cli/src/plugins/load-plugins.ts
+++ b/packages/cli/src/plugins/load-plugins.ts
@@ -1,7 +1,7 @@
 import { Plugin } from "./types/plugin.types.js";
-import { Config } from "../config/config.schema.js";
+import { ResolvedConfig } from "../config/config.schema.js";
 
-export async function loadPlugins(config: Config): Promise<Plugin[]> {
+export async function loadPlugins(config: ResolvedConfig): Promise<Plugin[]> {
   const plugins: Plugin[] = [];
 
   for (const pluginConfig of config.plugins) {
diff --git a/packages/cli/src/plugins/plugin-manager.ts b/packages/cli/src/plugins/plugin-manager.ts
index cb669fe..80f95c3 100644
--- a/packages/cli/src/plugins/plugin-manager.ts
+++ b/packages/cli/src/plugins/plugin-manager.ts
@@ -4,7 +4,7 @@ import { MarkdownGenerator } from "../core/types/generator.types.js";
 import { createVitePressPlugin } from "./builtin/vitepress-plugin.js";
 import path from "path";
 
-import { Config } from "../config/config.schema.js";
+import { ResolvedConfig } from "../config/config.schema.js";
 
 export class PluginManager {
   private plugins: Plugin[] = [];
@@ -32,7 +32,7 @@ export class PluginManager {
     }, manifest);
   }
 
-  getGenerator(config: Config): MarkdownGenerator {
+  getGenerator(config: ResolvedConfig): MarkdownGenerator {
     const generatorConfig = config.commands.build.generator;
 
     if (generatorConfig.name === "vitepress") {
diff --git a/packages/cli/src/plugins/types/plugin.types.ts b/packages/cli/src/plugins/types/plugin.types.ts
index c3a633e..0010092 100644
--- a/packages/cli/src/plugins/types/plugin.types.ts
+++ b/packages/cli/src/plugins/types/plugin.types.ts
@@ -1,5 +1,5 @@
 import { SidebarItem } from "../../commands/build/manifest/manifest.js";
-import { Config } from "../../config/config.schema.js";
+import { ResolvedConfig } from "../../config/config.schema.js";
 import { MarkdownGenerator } from "../../core/types/generator.types.js";
 
 /**
@@ -15,7 +15,7 @@ import { MarkdownGenerator } from "../../core/types/generator.types.js";
  */
 export interface PluginContext {
   workspacePath?: string;
-  config?: Config;
+  config?: ResolvedConfig;
 }
 
 /**
diff --git a/packages/cli/src/tests/plugin/plugin-loader.spec.ts b/packages/cli/src/tests/plugin/plugin-loader.spec.ts
index d409b4c..3564dcc 100644
--- a/packages/cli/src/tests/plugin/plugin-loader.spec.ts
+++ b/packages/cli/src/tests/plugin/plugin-loader.spec.ts
@@ -1,7 +1,7 @@
 import { describe, it, expect, beforeEach, afterEach } from "vitest";
 import { loadPlugins } from "../../plugins/load-plugins.js";
 import { createE2EWorkspace, E2EWorkspace } from "../utils/create-e2e-workspace.js";
-import { Config } from "../../config/config.schema.js";
+import { configSchema } from "../../config/config.schema.js";
 import { SidebarItem } from "../../commands/build/manifest/manifest.js";
 import { MOCK_CONFIG } from "../__mock__/config.mock.js";
 
@@ -31,7 +31,7 @@ export default {
 `
     );
 
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -44,7 +44,7 @@ export default {
             (await import(`${workspace.root}/my-plugin.js`)).default,
         },
       ],
-    };
+    });
 
     const plugins = await loadPlugins(config);
 
@@ -70,7 +70,7 @@ export const myNamedPlugin = {
 `
     );
 
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -83,7 +83,7 @@ export const myNamedPlugin = {
             (await import(`${workspace.root}/named-plugin.js`)).myNamedPlugin,
         },
       ],
-    };
+    });
 
     const plugins = await loadPlugins(config);
 
@@ -94,7 +94,7 @@ export const myNamedPlugin = {
 
   it("should load inline plugin", async () => {
     const workspace = await createE2EWorkspace();
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -113,7 +113,7 @@ export const myNamedPlugin = {
           }),
         },
       ],
-    };
+    });
 
     const plugins = await loadPlugins(config);
 
@@ -124,14 +124,14 @@ export const myNamedPlugin = {
 
   it("should handle empty plugin list", async () => {
     const workspace = await createE2EWorkspace();
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
         root: workspace.root,
       },
       plugins: [],
-    };
+    });
 
     const plugins = await loadPlugins(config);
 
@@ -140,7 +140,7 @@ export const myNamedPlugin = {
 
   it("should throw error for missing plugin file", async () => {
     const workspace = await createE2EWorkspace();
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -153,7 +153,7 @@ export const myNamedPlugin = {
             (await import(`${workspace.root}/nonexistent.js`)).default,
         },
       ],
-    };
+    });
 
     await expect(loadPlugins(config)).rejects.toThrow(
       "Failed to load plugin 'missing-plugin'"
@@ -162,7 +162,7 @@ export const myNamedPlugin = {
 
   it("should throw error for plugin without path or hooks", async () => {
     const workspace = await createE2EWorkspace();
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -174,7 +174,7 @@ export const myNamedPlugin = {
           plugin: null as unknown as () => Promise<unknown>,
         },
       ],
-    };
+    });
 
     await expect(loadPlugins(config)).rejects.toThrow(
       "pluginConfig.plugin is not a function"
@@ -190,7 +190,7 @@ export default "not a plugin object";
 `
     );
 
-    const config: Config = {
+    const config = configSchema.parse({
       ...MOCK_CONFIG,
       project: {
         ...MOCK_CONFIG.project,
@@ -203,7 +203,7 @@ export default "not a plugin object";
             (await import(`${workspace.root}/invalid-plugin.js`)).default,
         },
       ],
-    };
+    });
 
     await expect(loadPlugins(config)).rejects.toThrow(
       "did not return a valid plugin object"