diff --git a/autoload/ale.vim b/autoload/ale.vim
index 189f1e46..ca75577a 100644
--- a/autoload/ale.vim
+++ b/autoload/ale.vim
@@ -125,12 +125,13 @@ function! ale#Var(buffer, variable_name) abort
 endfunction
 
 " Escape a string suitably for each platform.
-" shellescape() does not work on Windows.
+" shellescape does not work on Windows.
 function! ale#Escape(str) abort
     if fnamemodify(&shell, ':t') ==? 'cmd.exe'
         " FIXME: Fix shell escaping for Windows.
         return fnameescape(a:str)
     else
-        return shellescape(a:str)
+        " An extra space is used here to disable the custom-checks.
+        return shellescape (a:str)
     endif
 endfunction
diff --git a/custom-checks b/custom-checks
index 37d2840c..c4b329ca 100755
--- a/custom-checks
+++ b/custom-checks
@@ -63,6 +63,7 @@ check_errors() {
 if (( FIX_ERRORS )); then
     for directory in "${directories[@]}"; do
         sed -i "s/^\(function.*)\) *$/\1 abort/" "$directory"/**/*.vim
+        sed -i "s/shellescape(/ale#Escape(/" "$directory"/**/*.vim
     done
 fi
 
@@ -75,5 +76,6 @@ check_errors '^  [^ ]' 'Use four spaces, not two spaces'
 check_errors $'\t' 'Use four spaces, not tabs'
 # This check should prevent people from using a particular inconsistent name.
 check_errors 'let g:ale_\w\+_\w\+_args =' 'Name your option g:ale_<filetype>_<lintername>_options instead'
+check_errors 'shellescape(' 'Use ale#Escape instead of shellescape'
 
 exit $RETURN_CODE