diff --git a/configure.py b/configure.py
index <HASH>..<HASH> 100755
--- a/configure.py
+++ b/configure.py
@@ -133,7 +133,9 @@ class Bootstrap:
         return self.writer.newline()
 
     def variable(self, key, val):
-        self.vars[key] = self._expand(val)
+        # In bootstrap mode, we have no ninja process to catch /showIncludes
+        # output.
+        self.vars[key] = self._expand(val).replace('/showIncludes', '')
         return self.writer.variable(key, val)
 
     def rule(self, name, **kwargs):
@@ -308,10 +310,6 @@ if platform.is_msvc():
               '/DNOMINMAX', '/D_CRT_SECURE_NO_WARNINGS',
               '/D_HAS_EXCEPTIONS=0',
               '/DNINJA_PYTHON="%s"' % options.with_python]
-    if options.bootstrap:
-        # In bootstrap mode, we have no ninja process to catch /showIncludes
-        # output.
-        cflags.remove('/showIncludes')
     if platform.msvc_needs_fs():
         cflags.append('/FS')
     ldflags = ['/DEBUG', '/libpath:$builddir']
win: Only drop /showIncludes in bootstrap builds.
Fixes #<I>.