--- a/mesonbuild/coredata.py
+++ b/mesonbuild/coredata.py
@@ -375,18 +375,13 @@
         '''
         if option.endswith('dir') and os.path.isabs(value) and \
            option not in builtin_dir_noprefix_options:
-            # Value must be a subdir of the prefix
             # commonpath will always return a path in the native format, so we
             # must use pathlib.PurePath to do the same conversion before
             # comparing.
-            if os.path.commonpath([value, prefix]) != str(PurePath(prefix)):
-                m = 'The value of the {!r} option is {!r} which must be a ' \
-                    'subdir of the prefix {!r}.\nNote that if you pass a ' \
-                    'relative path, it is assumed to be a subdir of prefix.'
-                raise MesonException(m.format(option, value, prefix))
-            # Convert path to be relative to prefix
-            skip = len(prefix) + 1
-            value = value[skip:]
+            if os.path.commonpath([value, prefix]) == str(PurePath(prefix)):
+                # Convert path to be relative to prefix
+                skip = len(prefix) + 1
+                value = value[skip:]
         return value
 
     def init_builtins(self):