diff --git a/emcc.py b/emcc.py
index 6c457f875ed2e..6f5838d6d6ebb 100644
--- a/emcc.py
+++ b/emcc.py
@@ -1260,7 +1260,7 @@ def run(args):
 
   ## Process argument and setup the compiler
   state = EmccState(args)
-  options, newargs = phase_parse_arguments(state)
+  options, phase1_args = phase_parse_arguments(state)
 
   if not shared.SKIP_SUBPROCS:
     shared.check_sanity()
@@ -1282,7 +1282,7 @@ def run(args):
   # settings until we reach the linking phase.
   settings.limit_settings(COMPILE_TIME_SETTINGS)
 
-  newargs, input_files = phase_setup(options, state, newargs)
+  newargs, input_files = phase_setup(options, state, phase1_args)
 
   if '-dumpmachine' in newargs or '-print-target-triple' in newargs or '--print-target-triple' in newargs:
     print(shared.get_llvm_target())
@@ -1627,8 +1627,6 @@ def phase_setup(options, state, newargs):
     elif '-M' in newargs or '-MM' in newargs:
       options.default_object_extension = '.mout' # not bitcode, not js; but just dependency rule of the input file
 
-    if options.output_file and len(input_files) > 1:
-      exit_with_error('cannot specify -o with -c/-S/-E/-M and multiple source files')
   else:
     for arg in state.orig_args:
       if any(arg.startswith(f) for f in COMPILE_ONLY_FLAGS):
@@ -3064,40 +3062,52 @@ def get_language_mode(args):
   language_mode = get_language_mode(newargs)
   use_cxx = 'c++' in language_mode or run_via_emxx
 
-  def get_clang_command(src_file):
-    return compiler + get_cflags(state.orig_args, use_cxx) + compile_args + [src_file]
+  def get_clang_command():
+    return compiler + get_cflags(state.orig_args, use_cxx) + compile_args
 
-  def get_clang_command_preprocessed(src_file):
-    return compiler + get_clang_flags(state.orig_args) + compile_args + [src_file]
+  def get_clang_command_preprocessed():
+    return compiler + get_clang_flags(state.orig_args) + compile_args
 
-  def get_clang_command_asm(src_file):
-    return compiler + get_target_flags() + compile_args + [src_file]
+  def get_clang_command_asm():
+    return compiler + get_target_flags() + compile_args
 
   # preprocessor-only (-E) support
   if state.mode == Mode.PREPROCESS_ONLY:
-    for input_file in [x[1] for x in input_files]:
-      cmd = get_clang_command(input_file)
-      if options.output_file:
-        cmd += ['-o', options.output_file]
-      # Do not compile, but just output the result from preprocessing stage or
-      # output the dependency rule. Warning: clang and gcc behave differently
-      # with -MF! (clang seems to not recognize it)
-      logger.debug(('just preprocessor ' if state.has_dash_E else 'just dependencies: ') + ' '.join(cmd))
-      shared.check_call(cmd)
+    inputs = [i[1] for i in input_files]
+    cmd = get_clang_command() + inputs
+    if options.output_file:
+      cmd += ['-o', options.output_file]
+    # Do not compile, but just output the result from preprocessing stage or
+    # output the dependency rule. Warning: clang and gcc behave differently
+    # with -MF! (clang seems to not recognize it)
+    logger.debug(('just preprocessor ' if state.has_dash_E else 'just dependencies: ') + ' '.join(cmd))
+    shared.check_call(cmd)
     return []
 
   # Precompiled headers support
   if state.mode == Mode.PCH:
-    headers = [header for _, header in input_files]
-    for header in headers:
+    inputs = [i[1] for i in input_files]
+    for header in inputs:
       if not shared.suffix(header) in HEADER_ENDINGS:
         exit_with_error(f'cannot mix precompiled headers with non-header inputs: {headers} : {header}')
-      cmd = get_clang_command(header)
-      if options.output_file:
-        cmd += ['-o', options.output_file]
-      logger.debug(f"running (for precompiled headers): {cmd[0]} {' '.join(cmd[1:])}")
-      shared.check_call(cmd)
-      return []
+    cmd = get_clang_command() + inputs
+    if options.output_file:
+      cmd += ['-o', options.output_file]
+    logger.debug(f"running (for precompiled headers): {cmd[0]} {' '.join(cmd[1:])}")
+    shared.check_call(cmd)
+    return []
+
+  if state.mode == Mode.COMPILE_ONLY:
+    inputs = [i[1] for i in input_files]
+    if all(get_file_suffix(i) in ASSEMBLY_ENDINGS for i in inputs):
+      cmd = get_clang_command_asm()
+    else:
+      cmd = get_clang_command()
+    if options.output_file:
+      cmd += ['-o', options.output_file]
+    cmd += inputs
+    shared.check_call(cmd)
+    return []
 
   linker_inputs = []
   seen_names = {}
@@ -3127,13 +3137,14 @@ def compile_source_file(i, input_file):
     if state.mode not in (Mode.COMPILE_ONLY, Mode.PREPROCESS_ONLY):
       linker_inputs.append((i, output_file))
     if get_file_suffix(input_file) in ASSEMBLY_ENDINGS:
-      cmd = get_clang_command_asm(input_file)
+      cmd = get_clang_command_asm()
     elif get_file_suffix(input_file) in PREPROCESSED_ENDINGS:
-      cmd = get_clang_command_preprocessed(input_file)
+      cmd = get_clang_command_preprocessed()
     else:
-      cmd = get_clang_command(input_file)
+      cmd = get_clang_command()
       if get_file_suffix(input_file) in ['.pcm']:
         cmd = [c for c in cmd if not c.startswith('-fprebuilt-module-path=')]
+    cmd += [input_file]
     if not state.has_dash_c:
       cmd += ['-c']
     cmd += ['-o', output_file]