diff --git a/.chronus/changes/fix-nested-options-2025-2-26-17-11-41.md b/.chronus/changes/fix-nested-options-2025-2-26-17-11-41.md
new file mode 100644
index 00000000000..186a3b115fc
--- /dev/null
+++ b/.chronus/changes/fix-nested-options-2025-2-26-17-11-41.md
@@ -0,0 +1,7 @@
+---
+changeKind: fix
+packages:
+  - "@typespec/compiler"
+---
+
+Fix extra properties not validated in nested entries of the config
\ No newline at end of file
diff --git a/.chronus/changes/fix-nested-options-2025-2-26-22-18-28.md b/.chronus/changes/fix-nested-options-2025-2-26-22-18-28.md
new file mode 100644
index 00000000000..537a77e4e42
--- /dev/null
+++ b/.chronus/changes/fix-nested-options-2025-2-26-22-18-28.md
@@ -0,0 +1,8 @@
+---
+# Change versionKind to one of: internal, fix, dependencies, feature, deprecation, breaking
+changeKind: fix
+packages:
+  - "@typespec/compiler"
+---
+
+Fix passing nested emitter options with `--option`
diff --git a/.chronus/changes/fix-nested-options-2025-2-28-17-33-1.md b/.chronus/changes/fix-nested-options-2025-2-28-17-33-1.md
new file mode 100644
index 00000000000..da2e23b20e8
--- /dev/null
+++ b/.chronus/changes/fix-nested-options-2025-2-28-17-33-1.md
@@ -0,0 +1,11 @@
+---
+# Change versionKind to one of: internal, fix, dependencies, feature, deprecation, breaking
+changeKind: internal
+packages:
+  - "@typespec/http-client-js"
+  - "@typespec/http-server-js"
+  - "@typespec/http-server-csharp"
+  - "@typespec/http-specs"
+---
+
+Fix nested options
diff --git a/packages/compiler/src/config/config-schema.ts b/packages/compiler/src/config/config-schema.ts
index 8c2b615e750..0df1c8b9333 100644
--- a/packages/compiler/src/config/config-schema.ts
+++ b/packages/compiler/src/config/config-schema.ts
@@ -28,6 +28,7 @@ export const TypeSpecConfigJsonSchema: JSONSchemaType<TypeSpecRawConfig> = {
           default: { type: "string" },
         },
         required: ["default"],
+        additionalProperties: false,
       },
     },
     parameters: {
@@ -40,6 +41,7 @@ export const TypeSpecConfigJsonSchema: JSONSchemaType<TypeSpecRawConfig> = {
           default: { type: "string" },
         },
         required: ["default"],
+        additionalProperties: false,
       },
     },
 
@@ -76,16 +78,6 @@ export const TypeSpecConfigJsonSchema: JSONSchemaType<TypeSpecRawConfig> = {
       required: [],
       additionalProperties: emitterOptionsSchema,
     },
-    emitters: {
-      type: "object",
-      nullable: true,
-      deprecated: true,
-      required: [],
-      additionalProperties: {
-        oneOf: [{ type: "boolean" }, emitterOptionsSchema],
-      },
-    },
-
     linter: {
       type: "object",
       nullable: true,
diff --git a/packages/compiler/src/config/config-to-options.ts b/packages/compiler/src/config/config-to-options.ts
index 322b6b372aa..24687261e52 100644
--- a/packages/compiler/src/config/config-to-options.ts
+++ b/packages/compiler/src/config/config-to-options.ts
@@ -142,28 +142,28 @@ function mergeOptions(
   overrides: Record<string, Record<string, unknown>> | undefined,
 ): Record<string, EmitterOptions> {
   const configuredEmitters: Record<string, Record<string, unknown>> = deepClone(base ?? {});
-  function deepMerge(emitter: any, options: any, name: string): any {
-    if (typeof emitter !== "object") {
-      return emitter;
-    }
-    for (const key of Object.keys(emitter)) {
-      if (hasNestedObjects(emitter[key])) {
-        emitter[key] = deepMerge(emitter[key], options, `${name}.${key}`);
-      } else if (typeof options[name] === "object") {
-        emitter[key] = options[name][key] ?? emitter[key];
+  function isObject(item: unknown): item is Record<string, unknown> {
+    return item && typeof item === "object" && (!Array.isArray(item) as any);
+  }
+  function deepMerge(target: any, source: any): any {
+    if (isObject(target) && isObject(source)) {
+      for (const key in source) {
+        if (isObject(source[key])) {
+          if (!target[key]) Object.assign(target, { [key]: {} });
+          deepMerge(target[key], source[key]);
+        } else {
+          Object.assign(target, { [key]: source[key] });
+        }
       }
     }
-    return emitter;
+
+    return target;
   }
 
   for (const [emitterName, cliOptionOverride] of Object.entries(overrides ?? {})) {
     configuredEmitters[emitterName] = deepMerge(
-      {
-        ...(configuredEmitters[emitterName] ?? {}),
-        ...cliOptionOverride,
-      },
-      overrides,
-      emitterName,
+      configuredEmitters[emitterName] ?? {},
+      cliOptionOverride,
     );
   }
 
diff --git a/packages/compiler/src/config/types.ts b/packages/compiler/src/config/types.ts
index b9aaf93af1f..f38d07a1173 100644
--- a/packages/compiler/src/config/types.ts
+++ b/packages/compiler/src/config/types.ts
@@ -86,7 +86,6 @@ export interface TypeSpecRawConfig {
 
   emit?: string[];
   options?: Record<string, EmitterOptions>;
-  emitters?: Record<string, boolean | EmitterOptions>;
 
   linter?: LinterConfig;
 }
diff --git a/packages/compiler/src/core/cli/actions/compile/args.ts b/packages/compiler/src/core/cli/actions/compile/args.ts
index 04b9863ac2b..b1e236e4a8e 100644
--- a/packages/compiler/src/core/cli/actions/compile/args.ts
+++ b/packages/compiler/src/core/cli/actions/compile/args.ts
@@ -1,9 +1,10 @@
 import { resolveCompilerOptions } from "../../../../config/config-to-options.js";
 import { omitUndefined } from "../../../../utils/misc.js";
 import { createDiagnosticCollector } from "../../../diagnostics.js";
+import { createDiagnostic } from "../../../messages.js";
 import { CompilerOptions } from "../../../options.js";
 import { resolvePath } from "../../../path-utils.js";
-import { CompilerHost, Diagnostic } from "../../../types.js";
+import { CompilerHost, Diagnostic, NoTarget } from "../../../types.js";
 
 export interface CompileCliArgs {
   path?: string;
@@ -42,7 +43,7 @@ export async function getCompilerOptions(
       : resolvePath(cwd, pathArg)
     : undefined;
 
-  const cliOptions = resolveCliOptions(args);
+  const cliOptions = diagnostics.pipe(resolveCliOptions(args));
   const resolvedOptions = diagnostics.pipe(
     await resolveCompilerOptions(host, {
       entrypoint,
@@ -89,20 +90,30 @@ function resolveConfigArgs(args: CompileCliArgs): Record<string, string> {
 
   return map;
 }
-function resolveCliOptions(args: CompileCliArgs): {
-  options: Record<string, Record<string, unknown>>;
-  miscOptions: Record<string, string> | undefined;
-} {
+
+function resolveCliOptions(args: CompileCliArgs): [
+  {
+    options: Record<string, Record<string, unknown>>;
+    miscOptions: Record<string, string> | undefined;
+  },
+  readonly Diagnostic[],
+] {
+  const diagnostics: Diagnostic[] = [];
   let miscOptions: Record<string, string> | undefined;
-  const options: Record<string, Record<string, string>> = {};
+  const options: Record<string, any> = {};
   for (const option of args.options ?? []) {
     const optionParts = option.split("=");
     if (optionParts.length !== 2) {
-      throw new Error(
-        `The --option parameter value "${option}" must be in the format: <emitterName>.some-options=value`,
+      diagnostics.push(
+        createDiagnostic({
+          code: "invalid-option-flag",
+          target: NoTarget,
+          format: { value: option },
+        }),
       );
+      continue;
     }
-    let optionKeyParts = optionParts[0].split(".");
+    const optionKeyParts = optionParts[0].split(".");
     if (optionKeyParts.length === 1) {
       const key = optionKeyParts[0];
       if (miscOptions === undefined) {
@@ -110,19 +121,21 @@ function resolveCliOptions(args: CompileCliArgs): {
       }
       miscOptions[key] = optionParts[1];
       continue;
-    } else if (optionKeyParts.length > 2) {
-      // support emitter/path/file.js.option=xyz
-      optionKeyParts = [
-        optionKeyParts.slice(0, -1).join("."),
-        optionKeyParts[optionKeyParts.length - 1],
-      ];
     }
-    const emitterName = optionKeyParts[0];
-    const key = optionKeyParts[1];
-    if (!(emitterName in options)) {
-      options[emitterName] = {};
+
+    let current: any = options;
+    for (let i = 0; i < optionKeyParts.length; i++) {
+      const part = optionKeyParts[i];
+      if (i === optionKeyParts.length - 1) {
+        current[part] = optionParts[1];
+      } else {
+        if (!current[part]) {
+          current[part] = {};
+        }
+        current = current[part];
+      }
     }
-    options[emitterName][key] = optionParts[1];
   }
-  return { options, miscOptions };
+
+  return [{ options, miscOptions }, diagnostics];
 }
diff --git a/packages/compiler/src/core/cli/utils.ts b/packages/compiler/src/core/cli/utils.ts
index c42e35b41bc..a536f0de515 100644
--- a/packages/compiler/src/core/cli/utils.ts
+++ b/packages/compiler/src/core/cli/utils.ts
@@ -28,11 +28,23 @@ export interface CliHostArgs {
 }
 
 export function withCliHost<T extends CliHostArgs>(
-  fn: (host: CliCompilerHost, args: T) => void | Promise<void>,
-): (args: T) => void | Promise<void> {
-  return (args: T) => {
+  fn: (host: CliCompilerHost, args: T) => Promise<void>,
+): (args: T) => Promise<void> {
+  return withFailsafe((args: T) => {
     const host = createCLICompilerHost(args);
     return fn(host, args);
+  });
+}
+
+function withFailsafe<T extends unknown[], R>(
+  fn: (...args: T) => Promise<R>,
+): (...args: T) => Promise<R> {
+  return async (...args: T) => {
+    try {
+      return await fn(...args);
+    } catch (error) {
+      handleInternalCompilerError(error);
+    }
   };
 }
 
@@ -42,7 +54,7 @@ export function withCliHost<T extends CliHostArgs>(
 export function withCliHostAndDiagnostics<T extends CliHostArgs>(
   fn: (host: CliCompilerHost, args: T) => readonly Diagnostic[] | Promise<readonly Diagnostic[]>,
 ): (args: T) => void | Promise<void> {
-  return async (args: T) => {
+  return withFailsafe(async (args: T) => {
     const host = createCLICompilerHost(args);
     const diagnostics = await fn(host, args);
     logDiagnostics(diagnostics, host.logSink);
@@ -50,7 +62,7 @@ export function withCliHostAndDiagnostics<T extends CliHostArgs>(
     if (diagnostics.some((d) => d.severity === "error")) {
       process.exit(1);
     }
-  };
+  });
 }
 
 export function createCLICompilerHost(options: CliHostArgs): CliCompilerHost {
@@ -169,7 +181,7 @@ export function logInternalCompilerError(error: unknown) {
  *
  * @param error error thrown
  */
-export function handleInternalCompilerError(error: unknown) {
+export function handleInternalCompilerError(error: unknown): never {
   logInternalCompilerError(error);
   process.exit(1);
 }
diff --git a/packages/compiler/src/core/messages.ts b/packages/compiler/src/core/messages.ts
index 33b68d93cd5..5c42d275d59 100644
--- a/packages/compiler/src/core/messages.ts
+++ b/packages/compiler/src/core/messages.ts
@@ -1059,6 +1059,12 @@ const diagnostics = {
       osx: "Couldn't find VS Code 'code' command in PATH. Make sure you have the VS Code executable added to the system PATH.\nSee instruction for Mac OS here https://code.visualstudio.com/docs/setup/mac",
     },
   },
+  "invalid-option-flag": {
+    severity: "error",
+    messages: {
+      default: paramMessage`The --option parameter value "${"value"}" must be in the format: <emitterName>.some-options=value`,
+    },
+  },
   // #endregion CLI
 } as const;
 
diff --git a/packages/compiler/test/cli.test.ts b/packages/compiler/test/cli.test.ts
index 872f2e77977..b4b85ba91d1 100644
--- a/packages/compiler/test/cli.test.ts
+++ b/packages/compiler/test/cli.test.ts
@@ -45,6 +45,23 @@ describe("compiler: cli", () => {
       });
     });
 
+    it("error if option doesn't have =", async () => {
+      const [_, diagnostics] = await getCompilerOptions(
+        host.compilerHost,
+        "ws/main.tsp",
+        cwd,
+        {
+          options: [`my-emitter.bar`],
+        },
+        {},
+      );
+
+      expectDiagnostics(diagnostics, {
+        code: "invalid-option-flag",
+        message: `The --option parameter value "my-emitter.bar" must be in the format: <emitterName>.some-options=value`,
+      });
+    });
+
     it("--option without an emitter are moved to miscOptions", async () => {
       const options = await resolveCompilerOptions({
         options: [`test-debug=true`],
@@ -54,6 +71,26 @@ describe("compiler: cli", () => {
       deepStrictEqual(options?.options, {});
     });
 
+    it("--option allows root level options", async () => {
+      const options = await resolveCompilerOptions({
+        options: [`my-emitter.foo=abc`],
+      });
+
+      deepStrictEqual(options?.options, {
+        "my-emitter": { foo: "abc" },
+      });
+    });
+
+    it("--option allows nested options", async () => {
+      const options = await resolveCompilerOptions({
+        options: [`my-emitter.foo.bar=abc`],
+      });
+
+      deepStrictEqual(options?.options, {
+        "my-emitter": { foo: { bar: "abc" } },
+      });
+    });
+
     describe("config file with emitters", () => {
       beforeEach(() => {
         host.addTypeSpecFile(
@@ -106,17 +143,6 @@ describe("compiler: cli", () => {
         );
       });
 
-      it("override emitter-output-dir from cli args using path to emitter with extension", async () => {
-        const options = await resolveCompilerOptions({
-          options: [`path/to/emitter.js.emitter-output-dir={cwd}/relative-to-cwd`],
-        });
-
-        strictEqual(
-          options?.options?.["path/to/emitter.js"]?.["emitter-output-dir"],
-          `${cwd}/relative-to-cwd`,
-        );
-      });
-
       describe("arg interpolation", () => {
         it("use default arg value", async () => {
           const options = await resolveCompilerOptions({});
diff --git a/packages/compiler/test/config/config.test.ts b/packages/compiler/test/config/config.test.ts
index a30a339b035..abc4fca5b6d 100644
--- a/packages/compiler/test/config/config.test.ts
+++ b/packages/compiler/test/config/config.test.ts
@@ -153,18 +153,18 @@ describe("compiler: config file loading", () => {
     });
 
     it("fails if passing the wrong type", () => {
-      deepStrictEqual(validate({ emitters: true } as any), [
+      deepStrictEqual(validate({ emit: true } as any), [
         {
           code: "invalid-schema",
           target: { file, pos: 0, end: 0 },
           severity: "error",
-          message: "Schema violation: must be object (/emitters)",
+          message: "Schema violation: must be array (/emit)",
         },
       ]);
     });
 
     it("succeeds if config is valid", () => {
-      deepStrictEqual(validate({ emitters: { openapi: {} } }), []);
+      deepStrictEqual(validate({ options: { openapi: {} } }), []);
     });
   });
 });
diff --git a/packages/compiler/test/config/resolve-compiler-option.test.ts b/packages/compiler/test/config/resolve-compiler-option.test.ts
index ac5d318202d..75a64ab0c92 100644
--- a/packages/compiler/test/config/resolve-compiler-option.test.ts
+++ b/packages/compiler/test/config/resolve-compiler-option.test.ts
@@ -49,7 +49,7 @@ describe("compiler: resolve compiler options", () => {
         options: {
           description: {
             name: "Testing name: Sphere",
-            details: { one: "Type: Bar", two: { "two-one": "Default: Metadata default" } },
+            details: { one: "Type: Microsoft", two: { "two-one": "Default: Microsoft" } },
           },
         },
         outputDir: tspOutputPath,
diff --git a/packages/compiler/test/config/scenarios/custom/myConfigNested.yaml b/packages/compiler/test/config/scenarios/custom/myConfigNested.yaml
index 9d6ce41cf72..8ebf740d4d9 100644
--- a/packages/compiler/test/config/scenarios/custom/myConfigNested.yaml
+++ b/packages/compiler/test/config/scenarios/custom/myConfigNested.yaml
@@ -4,14 +4,12 @@ emit:
 parameters:
   service-name:
     default: "Sphere"
-  metadata:
-    bar: "Bar"
-    Owner: "Microsoft"
-    default: "Metadata default"
+  owner:
+    default: "Microsoft"
 options:
   description:
     name: "Testing name: {service-name}"
     details:
-      one: "Type: {metadata.bar}"
+      one: "Type: {owner}"
       two:
-        two-one: "Default: {metadata.default}"
+        two-one: "Default: {owner}"
diff --git a/packages/compiler/test/e2e/cli/cli.e2e.ts b/packages/compiler/test/e2e/cli/cli.e2e.ts
index 43391e70670..e4c0ad4e5a1 100644
--- a/packages/compiler/test/e2e/cli/cli.e2e.ts
+++ b/packages/compiler/test/e2e/cli/cli.e2e.ts
@@ -215,7 +215,7 @@ describe("compile", () => {
         "--arg",
         "custom-dir=custom-dir-name",
         "--arg",
-        "metadata.owner=TypeSpec",
+        "owner=TypeSpec",
         "--option",
         "description.name=TypeSpec with options",
         "--option",
@@ -231,7 +231,7 @@ describe("compile", () => {
     );
     expect(file.toString()).toContain(`By Owner: TypeSpec
 TypeSpec with options
-Succeeded: TypeSpec with options with this short example by TypeSpec
+Succeeded: TypeSpec with options by TypeSpec
 Owner: TypeSpec
 Co-owner is defined by this test`);
   });
diff --git a/packages/compiler/test/e2e/cli/scenarios/with-option/tspconfig.yaml b/packages/compiler/test/e2e/cli/scenarios/with-option/tspconfig.yaml
index 04fffe5aae9..67f759575a9 100644
--- a/packages/compiler/test/e2e/cli/scenarios/with-option/tspconfig.yaml
+++ b/packages/compiler/test/e2e/cli/scenarios/with-option/tspconfig.yaml
@@ -3,23 +3,19 @@ parameters:
     default: default-value
   service-name:
     default: "TypeSpec"
-  metadata:
-    name: "Bar"
-    owner: "None"
-    description: "this short example"
-    default: "Metadata default"
+  argName:
+    default: "Bar"
+  owner:
+    default: "None"
 
 options:
   description:
     header: "By {description.by.owners.primary}"
-    name: "Testing name: {metadata.name}"
-    details: "Succeeded: {name} with {metadata.description} by {metadata.owner}"
+    name: "Testing name: {argName}"
+    details: "Succeeded: {name} by {owner}"
     by:
       owners:
-        primary: "Owner: {metadata.owner}"
+        primary: "Owner: {owner}"
         secondary: "Undefined secondary owner"
 
-emit:
-  - ./emitter.js
-
 output-dir: "{project-root}/tsp-output/{custom-dir}"
diff --git a/packages/http-client-js/eng/scripts/tspconfig.yaml b/packages/http-client-js/eng/scripts/tspconfig.yaml
index 3734bfa6b4c..a758e05bebd 100644
--- a/packages/http-client-js/eng/scripts/tspconfig.yaml
+++ b/packages/http-client-js/eng/scripts/tspconfig.yaml
@@ -1,5 +1,5 @@
-emitters:
-  "@typespec/http-client-js": true
+emit:
+  - "@typespec/http-client-js"
 
 options:
   "@typespec/http-client-js":
diff --git a/packages/http-server-csharp/eng/scripts/tspconfig.yaml b/packages/http-server-csharp/eng/scripts/tspconfig.yaml
index 7216934b25d..3ae534ee9c1 100644
--- a/packages/http-server-csharp/eng/scripts/tspconfig.yaml
+++ b/packages/http-server-csharp/eng/scripts/tspconfig.yaml
@@ -3,9 +3,9 @@ parameters:
     default: "8080"
   service-port-https:
     default: "8443"
-emitters:
-  "@typespec/http-server-csharp": true
-  "@typespec/openapi3": true
+emit:
+  - "@typespec/http-server-csharp"
+  - "@typespec/openapi3"
 options:
   "@typespec/http-server-csharp":
     emitter-output-dir: "{output-dir}"
diff --git a/packages/http-server-js/eng/scripts/tspconfig.yaml b/packages/http-server-js/eng/scripts/tspconfig.yaml
index 4b2afedea14..f1a34f59696 100644
--- a/packages/http-server-js/eng/scripts/tspconfig.yaml
+++ b/packages/http-server-js/eng/scripts/tspconfig.yaml
@@ -1,5 +1,5 @@
-emitters:
-  "@typespec/http-server-js": true
+emit:
+  - "@typespec/http-server-js"
 
 options:
   "@typespec/http-server-js":
diff --git a/packages/http-specs/tspconfig.yaml b/packages/http-specs/tspconfig.yaml
index e86cb1f4c20..e69de29bb2d 100644
--- a/packages/http-specs/tspconfig.yaml
+++ b/packages/http-specs/tspconfig.yaml
@@ -1,2 +0,0 @@
-emitters:
-  "@typespec/openapi3": true