diff --git a/doc/yaml_configuration.md b/doc/yaml_configuration.md
index 5bc153a41c..b5a673d123 100644
--- a/doc/yaml_configuration.md
+++ b/doc/yaml_configuration.md
@@ -437,6 +437,8 @@ Specify a variant binary distribution of GHC to use.  Known values:
   [setup-info](#setup-info) so `stack setup` knows where to download it, or
   pass the `stack setup --ghc-bindist` argument on the command-line
 
+This option is incompatible with `system-ghc: true`.
+
 ### setup-info
 
 (Since 0.1.5)
diff --git a/src/Stack/Config.hs b/src/Stack/Config.hs
index 0287c12040..b731627b53 100644
--- a/src/Stack/Config.hs
+++ b/src/Stack/Config.hs
@@ -226,9 +226,12 @@ configFromConfigMonoid configStackRoot configUserConfigPath mresolver mproject C
             configMonoidPackageIndices
 
          configGHCVariant0 = getFirst configMonoidGHCVariant
-
          configSystemGHC = fromFirst False configMonoidSystemGHC
-         configInstallGHC = fromFirst False configMonoidInstallGHC
+
+     when (isJust configGHCVariant0 && configSystemGHC) $
+         throwM ManualGHCVariantSettingsAreIncompatibleWithSystemGHC
+
+     let configInstallGHC = fromFirst False configMonoidInstallGHC
          configSkipGHCCheck = fromFirst False configMonoidSkipGHCCheck
          configSkipMsys = fromFirst False configMonoidSkipMsys
 
diff --git a/src/Stack/Options.hs b/src/Stack/Options.hs
index 90923bdbf6..424de72ffa 100644
--- a/src/Stack/Options.hs
+++ b/src/Stack/Options.hs
@@ -861,7 +861,7 @@ ghcVariantParser hide =
         readGHCVariant
         (long "ghc-variant" <> metavar "VARIANT" <>
          help
-             "Specialized GHC variant, e.g. integersimple" <>
+             "Specialized GHC variant, e.g. integersimple (incompatible with --system-ghc)" <>
          hideMods hide
         )
   where
diff --git a/src/Stack/SetupCmd.hs b/src/Stack/SetupCmd.hs
index 34d9190399..ddfc04156a 100644
--- a/src/Stack/SetupCmd.hs
+++ b/src/Stack/SetupCmd.hs
@@ -46,7 +46,7 @@ setupParser = SetupCmdOpts
                       "The default is to install the version implied by the resolver.")))
     <*> OA.boolFlags False
             "reinstall"
-            "reinstalling GHC, even if available"
+            "reinstalling GHC, even if available (incompatible with --system-ghc)"
             OA.idm
     <*> OA.boolFlags False
             "upgrade-cabal"
diff --git a/src/Stack/Types/Config.hs b/src/Stack/Types/Config.hs
index 115e5c6c8c..139aac9320 100644
--- a/src/Stack/Types/Config.hs
+++ b/src/Stack/Types/Config.hs
@@ -1043,6 +1043,7 @@ data ConfigException
   | BadStackRoot (Path Abs Dir)
   | Won'tCreateStackRootInDirectoryOwnedByDifferentUser (Path Abs Dir) (Path Abs Dir) -- ^ @$STACK_ROOT@, parent dir
   | UserDoesn'tOwnDirectory (Path Abs Dir)
+  | ManualGHCVariantSettingsAreIncompatibleWithSystemGHC
   deriving Typeable
 instance Show ConfigException where
     show (ParseConfigFileException configFile exception) = concat
@@ -1138,6 +1139,13 @@ instance Show ConfigException where
         , T.unpack configMonoidAllowDifferentUserName
         , "' to disable this precaution."
         ]
+    show ManualGHCVariantSettingsAreIncompatibleWithSystemGHC = T.unpack $ T.concat
+        [ "stack can only control the "
+        , configMonoidGHCVariantName
+        , " of its own GHC installations. Please use '--no-"
+        , configMonoidSystemGHCName
+        , "'."
+        ]
 instance Exception ConfigException
 
 showOptions :: WhichSolverCmd -> String