diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index 6d30189ae89..74dd8a45e7e 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -362,6 +362,10 @@ def cython(filename, verbose=0, compile_message=False,
     Cython.Compiler.Options.annotate = annotate
     Cython.Compiler.Options.embed_pos_in_docstring = True
     Cython.Compiler.Options.pre_import = "sage.all" if sage_namespace else None
+    try:
+        Cython.Compiler.Options.source_root = os.environ['MESON_SOURCE_ROOT']
+    except KeyError:
+        pass
 
     extra_compile_args = ['-w']  # no warnings
     extra_link_args = []
diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
index 2e04bd80f87..4a83b8859c1 100644
--- a/src/sage_setup/command/sage_build_cython.py
+++ b/src/sage_setup/command/sage_build_cython.py
@@ -42,7 +42,7 @@ if ntl_prefix:
 # always appear in exception tracebacks (by default, this is a runtime
 # setting in Cython which causes some overhead every time an exception
 # is raised).
-extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1"]
+extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1", "-ffile-prefix-map=$(pwd)=."]
 extra_link_args = [ ]
 
 DEVEL = False