diff --git a/lib/command.js b/lib/command.js
index 47e84141..78e1522e 100644
--- a/lib/command.js
+++ b/lib/command.js
@@ -55,12 +55,27 @@
     return compileScripts();
   };
   compileScripts = function() {
-    var base, compile, source, _i, _len, _results;
-    _results = [];
+    var base, compile, source, unprocessed, _i, _j, _len, _len2, _results;
+    unprocessed = [];
     for (_i = 0, _len = sources.length; _i < _len; _i++) {
       source = sources[_i];
+      unprocessed[sources.indexOf(source)] = 1;
+    }
+    _results = [];
+    for (_j = 0, _len2 = sources.length; _j < _len2; _j++) {
+      source = sources[_j];
       base = path.join(source);
       compile = function(source, sourceIndex, topLevel) {
+        var remaining;
+        remaining = function() {
+          var total, x, _k, _len3;
+          total = 0;
+          for (_k = 0, _len3 = unprocessed.length; _k < _len3; _k++) {
+            x = unprocessed[_k];
+            total += x;
+          }
+          return total;
+        };
         return path.exists(source, function(exists) {
           if (topLevel && !exists) {
             throw new Error("File not found: " + source);
@@ -71,20 +86,23 @@
             }
             if (stats.isDirectory()) {
               return fs.readdir(source, function(err, files) {
-                var file, _j, _len2, _results2;
-                _results2 = [];
-                for (_j = 0, _len2 = files.length; _j < _len2; _j++) {
-                  file = files[_j];
-                  _results2.push(compile(path.join(source, file), sourceIndex));
+                var file, _k, _len3;
+                unprocessed[sourceIndex] += files.length;
+                for (_k = 0, _len3 = files.length; _k < _len3; _k++) {
+                  file = files[_k];
+                  compile(path.join(source, file), sourceIndex);
                 }
-                return _results2;
+                return unprocessed[sourceIndex] -= 1;
               });
             } else if (topLevel || path.extname(source) === '.coffee') {
               fs.readFile(source, function(err, code) {
+                unprocessed[sourceIndex] -= 1;
                 if (opts.join) {
                   contents[sourceIndex] = helpers.compact([contents[sourceIndex], code.toString()]).join('\n');
-                  if (helpers.compact(contents).length > 0) {
-                    return compileJoin();
+                  if (remaining() === 0) {
+                    if (helpers.compact(contents).length > 0) {
+                      return compileJoin();
+                    }
                   }
                 } else {
                   return compileScript(source, code.toString(), base);
@@ -93,6 +111,8 @@
               if (opts.watch && !opts.join) {
                 return watch(source, base);
               }
+            } else {
+              return unprocessed[sourceIndex] -= 1;
             }
           });
         });
diff --git a/src/command.coffee b/src/command.coffee
index 0e2f438e..0f9543e5 100644
--- a/src/command.coffee
+++ b/src/command.coffee
@@ -74,25 +74,38 @@ exports.run = ->
 # compile them. If a directory is passed, recursively compile all
 # '.coffee' extension source files in it and all subdirectories.
 compileScripts = ->
+  unprocessed = []
+  for source in sources
+    unprocessed[sources.indexOf(source)]=1
   for source in sources
     base = path.join(source)
     compile = (source, sourceIndex, topLevel) ->
+      remaining_files = ->
+        total = 0
+        total += x for x in unprocessed
+        total
       path.exists source, (exists) ->
         throw new Error "File not found: #{source}" if topLevel and not exists
         fs.stat source, (err, stats) ->
           throw err if err
           if stats.isDirectory()
             fs.readdir source, (err, files) ->
+              unprocessed[sourceIndex] += files.length
               for file in files
                 compile path.join(source, file), sourceIndex
+              unprocessed[sourceIndex] -= 1
           else if topLevel or path.extname(source) is '.coffee'
             fs.readFile source, (err, code) ->
+              unprocessed[sourceIndex] -= 1
               if opts.join
                 contents[sourceIndex] = helpers.compact([contents[sourceIndex], code.toString()]).join('\n')
-                compileJoin() if helpers.compact(contents).length > 0
+                if remaining_files() == 0
+                  compileJoin() if helpers.compact(contents).length > 0
               else
                 compileScript(source, code.toString(), base)
             watch source, base if opts.watch and not opts.join
+          else
+            unprocessed[sourceIndex] -= 1
     compile source, sources.indexOf(source), true
 
 # Compile a single source script, containing the given code, according to the