diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6dced4a3..252ece51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,8 @@ Any BREAKING CHANGE between minor versions will be documented here in upper case
 - `deno task serve --quiet` no longer logs the http server requests.
 - BREAKING: The `includes` option of `sass` plugin accepts only a string
   (previously `string[]` was also accepted).
+- BREAKING: Removed all `Deno.run` calls and replaced with the new `Deno.Command` API.
+  -  Removed the `ScriptOptions` argument of `lume.run()`.
 
 ### Fixed
 - `multilanguage` plugin:
diff --git a/ci.ts b/ci.ts
index b6cc2cc6..ca7f622c 100644
--- a/ci.ts
+++ b/ci.ts
@@ -55,20 +55,18 @@ export default async function main(args: string[]) {
   checkDenoVersion();
 
   const [lumeArgs, denoArgs] = await getArgs(args, quiet);
-  const process = Deno.run({
-    cmd: [
-      Deno.execPath(),
+  const { code } = new Deno.Command(Deno.execPath(), {
+    args: [
       "run",
       ...denoArgs,
       import.meta.resolve("./cli.ts"),
       ...lumeArgs,
     ],
-  });
+    stdout: "inherit",
+    stderr: "inherit",
+  }).outputSync();
 
-  const status = await process.status();
-  process.close();
-
-  if (!status.success) {
+  if (code !== 0) {
     addEventListener("unload", () => Deno.exit(1));
   }
 }
diff --git a/cli/build.ts b/cli/build.ts
index 1dbba6dc..d6a433ff 100644
--- a/cli/build.ts
+++ b/cli/build.ts
@@ -120,7 +120,11 @@ export async function build(
         windows: "explorer",
       };
 
-      Deno.run({ cmd: [commands[Deno.build.os], `http://localhost:${port}/`] });
+      new Deno.Command(commands[Deno.build.os], {
+        args: [`http://localhost:${port}/`],
+        stdout: "inherit",
+        stderr: "inherit",
+      }).output();
     }
 
     site.dispatchEvent({ type: "afterStartServer" });
diff --git a/cli/import_map.ts b/cli/import_map.ts
index c5284e68..d33167a9 100644
--- a/cli/import_map.ts
+++ b/cli/import_map.ts
@@ -66,17 +66,17 @@ export async function importMap(url: URL, plugins: string[] = []) {
   if (configFile) {
     console.log("Reloading Deno cache...");
 
-    const process = Deno.run({
-      cmd: [
-        Deno.execPath(),
+    const command = new Deno.Command(Deno.execPath(), {
+      args: [
         "cache",
         "--unstable",
         "--reload",
         configFile,
       ],
+      stdout: "inherit",
+      stderr: "inherit",
     });
 
-    await process.status();
-    process.close();
+    await command.output();
   }
 }
diff --git a/core.ts b/core.ts
index 0b9ce2e2..0ae3a85b 100644
--- a/core.ts
+++ b/core.ts
@@ -21,11 +21,7 @@ import type {
   EventOptions,
 } from "./core/events.ts";
 
-import type {
-  default as Scripts,
-  ScriptOptions,
-  ScriptOrFunction,
-} from "./core/scripts.ts";
+import type { default as Scripts, ScriptOrFunction } from "./core/scripts.ts";
 
 import type { default as FS, Entry, Loader } from "./core/fs.ts";
 import type Logger from "./core/logger.ts";
@@ -135,7 +131,6 @@ export type {
   RequestHandler,
   ScopeFilter,
   Scopes,
-  ScriptOptions,
   ScriptOrFunction,
   Scripts,
   Server,
diff --git a/core/scripts.ts b/core/scripts.ts
index f71d1006..45e50d5a 100644
--- a/core/scripts.ts
+++ b/core/scripts.ts
@@ -4,8 +4,8 @@ export interface Options {
   /** The logger to use */
   logger: Logger;
 
-  /** The default cwd for scripts */
-  options: ScriptOptions;
+  /** The current working directory */
+  cwd?: string;
 }
 
 /**
@@ -16,15 +16,15 @@ export default class Scripts {
   /** The logger to output messages in the terminal */
   logger: Logger;
 
-  /** The default options to execute the scripts */
-  options: ScriptOptions;
+  /** The current working directory */
+  cwd: string;
 
   /** All registered scripts and functions */
   scripts = new Map<string, ScriptOrFunction[]>();
 
   constructor(options: Options) {
     this.logger = options.logger;
-    this.options = options.options;
+    this.cwd = options.cwd || Deno.cwd();
   }
 
   /** Register one or more scripts under a specific name */
@@ -34,13 +34,10 @@ export default class Scripts {
 
   /** Run one or more commands */
   async run(
-    options: ScriptOptions,
     ...names: ScriptOrFunction[]
   ): Promise<boolean> {
-    options = { ...this.options, ...options };
-
     for (const name of names) {
-      const success = await this.#run(options, name);
+      const success = await this.#run(name);
 
       if (!success) {
         return false;
@@ -51,16 +48,16 @@ export default class Scripts {
   }
 
   /** Run an individual script or function */
-  async #run(options: ScriptOptions, name: ScriptOrFunction): Promise<unknown> {
+  async #run(name: ScriptOrFunction): Promise<unknown> {
     if (typeof name === "string" && this.scripts.has(name)) {
       this.logger.log(`⚡️ <green>${name}</green>`);
       const command = this.scripts.get(name)!;
-      return this.run(options, ...command);
+      return this.run(...command);
     }
 
     if (Array.isArray(name)) {
       const results = await Promise.all(
-        name.map((n) => this.#run(options, n)),
+        name.map((n) => this.#run(n)),
       );
       return results.every((success) => success);
     }
@@ -69,7 +66,7 @@ export default class Scripts {
       return this.#runFunction(name);
     }
 
-    return this.#runScript(options, name);
+    return this.#runScript(name);
   }
 
   /** Run a function */
@@ -82,15 +79,21 @@ export default class Scripts {
   }
 
   /** Run a shell command */
-  async #runScript(options: ScriptOptions, script: string) {
+  async #runScript(script: string) {
     this.logger.log(`⚡️ <dim>${script}</dim>`);
 
-    const cmd = shArgs(script);
-    const process = Deno.run({ cmd, ...options });
-    const status = await process.status();
-    process.close();
+    const args = shArgs(script);
+    const cmd = args.shift()!;
+
+    const command = new Deno.Command(cmd, {
+      args,
+      stdout: "inherit",
+      stderr: "inherit",
+      cwd: this.cwd,
+    });
 
-    return status.success;
+    const output = await command.output();
+    return output.code === 0;
   }
 }
 
@@ -103,6 +106,3 @@ function shArgs(script: string) {
 
 /** A script or function */
 export type ScriptOrFunction = string | (() => unknown) | ScriptOrFunction[];
-
-/** The options for a script */
-export type ScriptOptions = Omit<Deno.RunOptions, "cmd">;
diff --git a/core/site.ts b/core/site.ts
index f6ee6f0c..91ebfa64 100644
--- a/core/site.ts
+++ b/core/site.ts
@@ -36,7 +36,6 @@ import type {
   Plugin,
   Processor,
   ScopeFilter,
-  ScriptOptions,
   ScriptOrFunction,
   StaticFile,
 } from "../core.ts";
@@ -183,7 +182,7 @@ export default class Site {
     // Other stuff
     const events = new Events<SiteEvent>();
     const logger = new Logger({ quiet });
-    const scripts = new Scripts({ logger, options: { cwd } });
+    const scripts = new Scripts({ logger, cwd });
     const writer = new Writer({ src, dest, logger });
 
     // Save everything in the site instance
@@ -274,8 +273,8 @@ export default class Site {
   }
 
   /** Runs a script or function registered previously */
-  async run(name: string, options: ScriptOptions = {}): Promise<boolean> {
-    return await this.scripts.run(options, name);
+  async run(name: string): Promise<boolean> {
+    return await this.scripts.run(name);
   }
 
   /**