diff --git a/ale_linters/c/clang.vim b/ale_linters/c/clang.vim
index 25d9371..74279b7 100644
--- a/ale_linters/c/clang.vim
+++ b/ale_linters/c/clang.vim
@@ -3,7 +3,7 @@
 
 call ale#Set('c_clang_executable', 'clang')
 call ale#Set('c_clang_options', '-std=c11 -Wall')
-call ale#Set('c_gcc_parse_makefile', 0)
+call ale#Set('c_clang_parse_makefile', 0)
 
 function! ale_linters#c#clang#GetExecutable(buffer) abort
     return ale#Var(a:buffer, 'c_clang_executable')
@@ -11,11 +11,13 @@ endfunction
 
 function! ale_linters#c#clang#GetCommand(buffer) abort
 let l:cflags = []
-    if g:ale_c_parse_makefile
-        let l:cflags = join(ale#c#ParseMakefile(a:buffer), ' ')
+    if g:ale_c_clang_parse_makefile
+        let l:cflags = join(ale#c#ParseMakefile(a:buffer), ' ') . ' '
     endif
     if empty(l:cflags)
         let l:cflags = ale#c#IncludeOptions(ale#c#FindLocalHeaderPaths(a:buffer))
+    else
+        let l:cflags .= ' '
     endif
 
     " -iquote with the directory the file is in makes #include work for
@@ -23,7 +25,7 @@ let l:cflags = []
     return ale#Escape(ale_linters#c#clang#GetExecutable(a:buffer))
     \   . ' -S -x c -fsyntax-only '
     \   . '-iquote ' . ale#Escape(fnamemodify(bufname(a:buffer), ':p:h')) . ' '
-    \   . l:cflags . ' '
+    \   . l:cflags
     \   . ale#Var(a:buffer, 'c_clang_options') . ' -'
 endfunction
 
diff --git a/ale_linters/c/gcc.vim b/ale_linters/c/gcc.vim
index 3ad243a..3199fe8 100644
--- a/ale_linters/c/gcc.vim
+++ b/ale_linters/c/gcc.vim
@@ -3,7 +3,7 @@
 
 call ale#Set('c_gcc_executable', 'gcc')
 call ale#Set('c_gcc_options', '-std=c11 -Wall')
-call ale#Set('c_parse_makefile', 0)
+call ale#Set('c_gcc_parse_makefile', 0)
 
 function! ale_linters#c#gcc#GetExecutable(buffer) abort
     return ale#Var(a:buffer, 'c_gcc_executable')
@@ -11,11 +11,13 @@ endfunction
 
 function! ale_linters#c#gcc#GetCommand(buffer) abort
     let l:cflags = []
-    if g:ale_c_parse_makefile
+    if g:ale_c_gcc_parse_makefile
         let l:cflags = join(ale#c#ParseMakefile(a:buffer), ' ')
     endif
     if empty(l:cflags)
         let l:cflags = ale#c#IncludeOptions(ale#c#FindLocalHeaderPaths(a:buffer))
+    else
+        let l:cflags .= ' '
     endif
 
     " -iquote with the directory the file is in makes #include work for
@@ -23,7 +25,7 @@ function! ale_linters#c#gcc#GetCommand(buffer) abort
     return ale#Escape(ale_linters#c#gcc#GetExecutable(a:buffer))
     \   . ' -S -x c -fsyntax-only '
     \   . '-iquote ' . ale#Escape(fnamemodify(bufname(a:buffer), ':p:h')) . ' '
-    \   . l:cflags . ' '
+    \   . l:cflags
     \   . ale#Var(a:buffer, 'c_gcc_options') . ' -'
 endfunction
 
diff --git a/autoload/ale/c.vim b/autoload/ale/c.vim
index 4bf8ad4..7dc532b 100644
--- a/autoload/ale/c.vim
+++ b/autoload/ale/c.vim
@@ -24,42 +24,42 @@ endfunction
 
 function! ale#c#ParseCFlags(project_root, stdout_make) abort
     let l:cflags_list = []
-    let l:cflags = split(a:stdout_make, " ")
+    let l:cflags = split(a:stdout_make)
     let l:shell_option = 0
     let l:macro_option = 0
     let l:previous_option = ''
     for l:option in l:cflags
         " Check if cflag contained spaces
-        if l:shell_option || stridx(l:option, "=`") >= 0
+        if l:shell_option || stridx(l:option, '=`') >= 0
             " Cflag contained shell command with spaces (ex. -D='date +%s')
             let l:shell_option = 1
             let l:previous_option .= l:option . ' '
-            if l:option[-1: -1] != "`"
+            if l:option[-1: -1] isnot? '`'
                 continue
             endif
             let l:shell_option = 0
-        elseif l:macro_option || stridx(l:option, "$((") > 0
+        elseif l:macro_option || stridx(l:option, '$((') > 0
             " Cflag contained macro with spaces (ex -Da=$(( 4 * 20  )))
             let l:macro_option = 1
             let l:previous_option .= l:option . ' '
-            if stridx(l:option, "))") < 0
+            if stridx(l:option, '))') < 0
                 continue
             endif
             let l:macro_option = 0
         endif
-        if l:previous_option != ''
+        if l:previous_option isnot? ''
             let l:option = l:previous_option
             let l:previous_option = ''
         endif
         " Fix relative paths if needed
-        if stridx(l:option, "-I") >= 0
-            if stridx(l:option, "-I/") < 0
+        if stridx(l:option, '-I') >= 0
+            if stridx(l:option, '-I' . s:sep) < 0
                 let l:option = '-I' . a:project_root . s:sep . l:option[2:]
             endif
         endif
         " Parse the cflag
-        if stridx(l:option, "-I") >= 0 ||
-           \ stridx(l:option, "-D") >= 0
+        if stridx(l:option, '-I') >= 0 ||
+           \ stridx(l:option, '-D') >= 0
             if index(l:cflags_list, l:option) < 0
                 call add(l:cflags_list, l:option)
             endif
@@ -74,12 +74,12 @@ function! ale#c#ParseMakefile(buffer) abort
 
     if !empty(l:project_root)
         if !empty(globpath(l:project_root, 'Makefile', 0))
-            let stdout_make = system('cd '. l:project_root . ' && make -n')
-             for l:object in split(l:stdout_make, '\n')
-                 if stridx(l:object, expand("%t"))
-                     return ale#c#ParseCFlags(l:project_root, l:object)
-                 endif
-             endfor
+            let l:stdout_make = system('cd '. l:project_root . ' && make -n')
+            for l:object in split(l:stdout_make, '\n')
+                if stridx(l:object, expand('#' . a:buffer . '...'))
+                    return ale#c#ParseCFlags(l:project_root, l:object)
+                endif
+            endfor
         endif
     endif
     return []
diff --git a/test/test_c_parse_makefile.vader b/test/test_c_parse_makefile.vader
new file mode 100644
index 0000000..fac04bb
--- /dev/null
+++ b/test/test_c_parse_makefile.vader
@@ -0,0 +1,72 @@
+Before:
+  Save g:ale_c_gcc_options
+  Save g:ale_c_gcc_parse_makefile
+  Save g:ale_c_clang_options
+  Save g:ale_c_clang_parse_makefile
+  Save g:ale_cpp_gcc_options
+  Save g:ale_cpp_clang_options
+
+  call ale#test#SetDirectory('/testplugin/test')
+
+  let g:ale_c_gcc_parse_makefile=1
+  let g:ale_c_clang_parse_makefile=1
+  let g:ale_c_gcc_options = ''
+  let g:ale_c_clang_options = ''
+  let g:ale_cpp_gcc_options = ''
+  let g:ale_cpp_clang_options = ''
+
+After:
+  Restore
+
+  call ale#test#RestoreDirectory()
+  call ale#linter#Reset()
+
+" Run this only once for this series of tests. The cleanup Execute step
+" will run at the bottom of this file.
+"
+" We need to move .git/HEAD away so we don't match it, as we need to test
+" functions which look for .git/HEAD.
+Execute(Move .git/HEAD to a temp dir):
+  let g:temp_head_filename = tempname()
+  let g:head_filename = findfile('.git/HEAD', ';')
+
+  if !empty(g:head_filename)
+    call writefile(readfile(g:head_filename, 'b'), g:temp_head_filename, 'b')
+    call delete(g:head_filename)
+  endif
+
+Execute(The C GCC handler should include directories specified in the include path for projects with a Makefile):
+  runtime! ale_linters/c/gcc.vim
+
+  call ale#test#SetFilename('test_c_projects/makefile_project/subdir/file.c')
+
+  AssertEqual
+  \ ale#Escape('gcc')
+  \   . ' -S -x c -fsyntax-only '
+  \   . '-iquote ' . ale#Escape(ale#path#Simplify(g:dir .  '/test_c_projects/makefile_project/subdir'))
+  \   . ' -I' . ale#Escape(ale#path#Simplify(g:dir .  '/test_c_projects/makefile_project/subdir/'))[1:-3] . ' '
+  \   . ' -'
+  \ , ale_linters#c#gcc#GetCommand(bufnr(''))
+
+Execute(The C++ Clang handler should include directories specified in the include path for projects with a Makefile):
+  runtime! ale_linters/c/clang.vim
+
+  call ale#test#SetFilename('test_c_projects/makefile_project/subdir/file.c')
+
+  AssertEqual
+  \   ale#Escape('clang')
+  \   . ' -S -x c -fsyntax-only '
+  \   . '-iquote ' . ale#Escape(ale#path#Simplify(g:dir .  '/test_c_projects/makefile_project/subdir'))
+  \   . ' -I' . ale#Escape(ale#path#Simplify(g:dir .  '/test_c_projects/makefile_project/subdir'))[1:-2] . ' '
+  \   . ' -'
+  \ , ale_linters#c#clang#GetCommand(bufnr(''))
+
+
+Execute(Move .git/HEAD back):
+  if !empty(g:head_filename)
+    call writefile(readfile(g:temp_head_filename, 'b'), g:head_filename, 'b')
+    call delete(g:temp_head_filename)
+  endif
+
+  unlet! g:temp_head_filename
+  unlet! g:head_filename
diff --git a/test/test_c_projects/makefile_project/Makefile b/test/test_c_projects/makefile_project/Makefile
index e69de29..8b49a94 100644
--- a/test/test_c_projects/makefile_project/Makefile
+++ b/test/test_c_projects/makefile_project/Makefile
@@ -0,0 +1,3 @@
+file.o : subdir/file.c
+	cc -c subdir/file.c -Isubdir
+
diff --git a/test/test_c_projects/makefile_project/subdir/file.c b/test/test_c_projects/makefile_project/subdir/file.c
new file mode 100644
index 0000000..e69de29