diff --git a/src/Stack/Config.hs b/src/Stack/Config.hs
index d5662ad35d..2a7d21ef6b 100644
--- a/src/Stack/Config.hs
+++ b/src/Stack/Config.hs
@@ -126,7 +126,9 @@ configFromConfigMonoid configStackRoot mproject configMonoid@ConfigMonoid{..} =
                 }]
             configMonoidPackageIndices
 
-         configSystemGHC = fromMaybe True configMonoidSystemGHC
+         configGHCVariant0 = fmap parseGHCVariant configMonoidGHCVariant
+
+         configSystemGHC = fromMaybe (isNothing configGHCVariant0) configMonoidSystemGHC
          configInstallGHC = fromMaybe False configMonoidInstallGHC
          configSkipGHCCheck = fromMaybe False configMonoidSkipGHCCheck
          configSkipMsys = fromMaybe False configMonoidSkipMsys
@@ -143,8 +145,6 @@ configFromConfigMonoid configStackRoot mproject configMonoid@ConfigMonoid{..} =
             $ configMonoidOS >>= Distribution.Text.simpleParse
          configPlatform = Platform arch os
 
-         configGHCVariant0 = fmap parseGHCVariant configMonoidGHCVariant
-
          configRequireStackVersion = simplifyVersionRange configMonoidRequireStackVersion
 
          configConfigMonoid = configMonoid
diff --git a/src/Stack/Options.hs b/src/Stack/Options.hs
index 4a36afa23d..6f3340c9b5 100644
--- a/src/Stack/Options.hs
+++ b/src/Stack/Options.hs
@@ -243,7 +243,7 @@ configOptsParser docker =
     <*> optional (strOption
             ( long "ghc-variant"
            <> metavar "VARIANT"
-           <> help "Specialized GHC variant, e.g. integersimple"
+           <> help "Specialized GHC variant, e.g. integersimple (implies --no-system-ghc)"
             ))
     <*> optional (option auto
             ( long "jobs"