diff --git a/client.js b/client.js
index 444d6c0d..d0e6f96d 100644
--- a/client.js
+++ b/client.js
@@ -155,37 +155,56 @@ class Instance extends link.Link{
 		// Patch save with lua modules from plugins
 		console.log("Clusterio | Patching save");
 
-		// For now it's assumed that all files in the lua folder of a plugin is
-		// to be patched in under the name of the plugin and loaded for all
-		// plugins that are not disabled.  This will most likely change in the
-		// future when the plugin refactor is done.
-		let modules = [];
-		for (let pluginName of await fs.readdir("plugins")) {
-			let pluginDir = path.join("plugins", pluginName);
-			if (await fs.pathExists(path.join(pluginDir, "DISABLED"))) {
+		// Find plugin modules to patch in
+		let modules = new Map();
+		for (let pluginName of this.plugins.keys()) {
+			let modulePath = path.join('plugins', pluginName, 'module');
+			if (!await fs.pathExists(modulePath)) {
 				continue;
 			}
 
-			if (!await fs.pathExists(path.join(pluginDir, "lua"))) {
-				continue;
+			let moduleJsonPath = path.join(modulePath, 'module.json');
+			if (!await fs.pathExists(moduleJsonPath)) {
+				throw new Error(`Module for plugin ${pluginName} is missing module.json`);
 			}
 
-			let module = {
-				"name": pluginName,
-				"files": [],
-			};
-
-			for (let fileName of await fs.readdir(path.join(pluginDir, "lua"))) {
-				module["files"].push({
-					path: pluginName+"/"+fileName,
-					content: await fs.readFile(path.join(pluginDir, "lua", fileName)),
-					load: true,
-				});
+			let module = JSON.parse(await fs.readFile(moduleJsonPath));
+			if (module.name !== pluginName) {
+				throw new Error(`Expected name of module for plugin ${pluginName} to match the plugin name`);
 			}
 
-			modules.push(module);
+			module = Object.assign({
+				path: modulePath,
+				load: [],
+			}, module);
+			modules.set(module.name, module);
 		}
-		await factorio.patch(this.path("saves", saveName), modules);
+
+		for (let entry of await fs.readdir('modules', { withFileTypes: true })) {
+			if (entry.isDirectory()) {
+				if (modules.has(entry.name)) {
+					throw new Error(`Module with name ${entry.name} already exists in a plugin`);
+				}
+
+				let moduleJsonPath = path.join('modules', entry.name, 'module.json');
+				if (!await fs.pathExists(moduleJsonPath)) {
+					throw new Error(`Module ${entry.name} is missing module.json`);
+				}
+
+				let module = JSON.parse(await fs.readFile(moduleJsonPath));
+				if (module.name !== entry.name) {
+					throw new Error(`Expected name of module ${entry.name} to match the directory name`);
+				}
+
+				module = Object.assign({
+					path: path.join('modules', entry.name),
+					load: [],
+				}, module);
+				modules.set(module.name, module);
+			}
+		}
+
+		await factorio.patch(this.path("saves", saveName), modules.values());
 
 		this.server.on('rcon-ready', () => {
 			console.log("Clusterio | RCON connection established");
@@ -805,6 +824,7 @@ async function startClient() {
 
 	await fs.ensureDir(slaveConfig.instanceDirectory);
 	await fs.ensureDir("sharedMods");
+	await fs.ensureDir("modules");
 
 	// Set the process title, shows up as the title of the CMD window on windows
 	// and as the process name in ps/top on linux.
diff --git a/docs/developing-for-clusterio.md b/docs/developing-for-clusterio.md
index 5cf4958f..6083285e 100644
--- a/docs/developing-for-clusterio.md
+++ b/docs/developing-for-clusterio.md
@@ -180,13 +180,40 @@ for some pointers if you get stuck.
 Clusterio Modules
 -----------------
 
-Modules are primarily used by plugins to inject code into Factorio
-games with the save patcher.  The save patcher puts modules into the
-`modules` folder of the Factorio save and adds code to `control.lua` to
+Modules are primarily used by plugins to inject code into Factorio games
+with the save patcher, though it's also possible to make stand alone
+modules that are loaded into the game if you don't need the capabilites
+of the plugin system.  The save patcher puts modules into the `modules`
+folder of the Factorio save and adds code to `control.lua` to
 load the modules by requiring it and passing the result of the require
 call to the `add_lib` function of the event_handler lib.  See the
 section on the [event_handler interface](#event_handler-interface) for a
-detailed description on how this works.
+detailed description on how the event_handler lib works.
+
+Stand alone modules are placed into the modules folder of Clusterio,
+plugin modules are located in the module folder of the plugin.  In
+either case a `module.json` file is required and has the following
+structure:
+
+```json
+{
+    "name": "my_module",
+    "load": ["foo.lua"]
+}
+```
+
+The following entries are supported in the module.json file:
+
+- `name`:
+    Name of the module, must match the folder the module is located in
+    for stand alone modules or the name of the plugin the module is
+    located in.
+- `load`:
+    Lua files to load with the `event_handler` lib.  They should be
+    specified as paths that's relative to the module and uses forward
+    slashes as directory sepparators.  Thus foo.lua will require a file
+    by that name and feed the result of that require to the event
+    handler lib.
 
 Because modules can be patched into an existing game you cannot rely on
 the `on_init` callback to be called in Clusterio Modules.  Nor can you
@@ -194,11 +221,6 @@ rely on the `on_configuration_changed` callback, as this is not called
 when level code changes.  Instead you will have to initialize whatever
 global variable you need when you first use them.
 
-Currently any files in a folder named `lua` in a Clusterio plugin is
-assumed to be a module and will be patched into the save before starting
-up Factorio.  This will most likely change with the planned plugin
-restructuring.
-
 
 Clusterio Plugins
 -----------------
diff --git a/docs/writing-plugins.md b/docs/writing-plugins.md
index 86b450d6..9926e845 100644
--- a/docs/writing-plugins.md
+++ b/docs/writing-plugins.md
@@ -18,7 +18,8 @@ The basic file structure of a plugin is the following.
       +- instance.js
       +- test/
       |  +- plugin.js
-      +- lua/
+      +- module/
+         +- module.json
          +- plugin.lua
 
 The most important file is the `info.js` file.  Without it the plugin
@@ -70,6 +71,12 @@ The following properties are recognized:
     Object with link messages definitions for this plugin.  See guide
     for [defining link messages](#defining-link-messages) below.
 
+The optional module folder contains a Clusterio module that will be
+patched into the save when the plugin is enabled.  See the section on
+[Clusterio Modules](developing-for-clusterio.md) in the Developing for
+Clusterio document.  The only restriction imposed on modules embedded
+into plugins is that they must be named the same as the plugin.
+
 While there is no standard for how to organize a plugin it's recommended
 to put the MasterPlugin class definition into master.js and the
 InstancePlugin class definition into instance.js.  You can put them into
diff --git a/lib/factorio/patch.js b/lib/factorio/patch.js
index 235d53b5..41ebf1c0 100644
--- a/lib/factorio/patch.js
+++ b/lib/factorio/patch.js
@@ -7,6 +7,7 @@
 const events = require("events");
 const fs = require("fs-extra");
 const jszip = require("jszip");
+const path = require("path");
 
 const hash = require("lib/hash");
 
@@ -81,7 +82,7 @@ function generateLoader(patchInfo) {
 	for (let module of patchInfo["modules"]) {
 		for (let file of module["files"]) {
 			if (file["load"]) {
-				let requirePath = "modules/" + file["path"].slice(0, -4);
+				let requirePath = `modules/${module.name}/${file["path"].slice(0, -4)}`;
 				lines.push('event_handler.add_lib(require("'+requirePath+'"))');
 			}
 		}
@@ -135,19 +136,31 @@ async function patch(savePath, modules) {
 	}
 
 	// Add the modules to the save.
-	let modulesDir = root.folder("modules");
 	for (let module of modules) {
+		let moduleDir = root.folder(`modules/${module.name}`);
 		let moduleInfo = {
 			"name": module.name,
 			"files": [],
 		}
 
-		for (let file of module.files) {
-			modulesDir.file(file.path, file.content);
-			moduleInfo["files"].push({
-				"path": file.path,
-				"load": Boolean(file.load),
-			});
+		let dirs = [[module.path, '']];
+		while (dirs.length) {
+			let [dir, relativeDir] = dirs.pop();
+			for (let entry of await fs.readdir(dir, { withFileTypes: true })) {
+				let fsPath = path.join(dir, entry.name);
+				let relativePath = path.posix.join(relativeDir, entry.name);
+
+				if (entry.isFile()) {
+					moduleDir.file(relativePath, await fs.readFile(fsPath));
+					moduleInfo["files"].push({
+						"path": relativePath,
+						"load": module.load.includes(relativePath),
+					});
+
+				} else if (entry.isDirectory()) {
+					dirs.push([fsPath, relativePath]);
+				}
+			}
 		}
 
 		patchInfo["modules"].push(moduleInfo);
diff --git a/plugins/statistics_exporter/lua/export.lua b/plugins/statistics_exporter/module/export.lua
similarity index 100%
rename from plugins/statistics_exporter/lua/export.lua
rename to plugins/statistics_exporter/module/export.lua
diff --git a/plugins/statistics_exporter/module/module.json b/plugins/statistics_exporter/module/module.json
new file mode 100644
index 00000000..253cd328
--- /dev/null
+++ b/plugins/statistics_exporter/module/module.json
@@ -0,0 +1,4 @@
+{
+    "name": "statistics_exporter",
+    "load": ["export.lua"]
+}
diff --git a/plugins/statistics_exporter/slave.js b/plugins/statistics_exporter/slave.js
deleted file mode 100644
index e69de29b..00000000
diff --git a/test/file/modules/subdir/dir/test.lua b/test/file/modules/subdir/dir/test.lua
new file mode 100644
index 00000000..181e93bd
--- /dev/null
+++ b/test/file/modules/subdir/dir/test.lua
@@ -0,0 +1 @@
+-- test
diff --git a/test/file/modules/test/test.lua b/test/file/modules/test/test.lua
new file mode 100644
index 00000000..181e93bd
--- /dev/null
+++ b/test/file/modules/test/test.lua
@@ -0,0 +1 @@
+-- test
diff --git a/test/integration/patch.js b/test/integration/patch.js
index 25e8b1f8..9897bc28 100644
--- a/test/integration/patch.js
+++ b/test/integration/patch.js
@@ -23,18 +23,23 @@ describe("Integration of lib/factorio/patch", function() {
 			slowTest(this);
 			await factorio.patch(savePath, [{
 				name: "test",
-				files: [{ path: "test.lua", content: "-- test" }]
+				path: "test/file/modules/test",
+				load: [],
+			}, {
+				name: "subdir",
+				path: "test/file/modules/subdir",
+				load: [],
 			}]);
 
 			let zip = await jszip.loadAsync(await fs.readFile(savePath));
-			let content = await zip.file("test/modules/test.lua").async("string");
-			assert.equal(content, "-- test");
+			assert.equal(await zip.file("test/modules/test/test.lua").async("string"), "-- test\n");
+			assert.equal(await zip.file("test/modules/subdir/dir/test.lua").async("string"), "-- test\n");
 		});
 		it("should remove old modules in a save", async function() {
 			slowTest(this);
-			await factorio.patch(savePath, [{ name: "test", files: [] }]);
+			await factorio.patch(savePath, []);
 			let zip = await jszip.loadAsync(await fs.readFile(savePath));
-			assert.equal(zip.file("test/modules/test.lua"), null);
+			assert.equal(zip.file("test/modules/test/test.lua"), null);
 		});
 	});
 });
diff --git a/test/lib/factorio/patch.js b/test/lib/factorio/patch.js
index c9f3900f..3815a852 100644
--- a/test/lib/factorio/patch.js
+++ b/test/lib/factorio/patch.js
@@ -59,7 +59,7 @@ describe("lib/factorio", function() {
 			'event_handler.add_lib(require("foo"))',
 			'',
 			'-- Clusterio modules',
-			'event_handler.add_lib(require("modules/bar"))',
+			'event_handler.add_lib(require("modules/spam/bar"))',
 			'',
 		].join('\n');
 		let patchInfo = {