diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc
index d68e8b2bc..03a8f5080 100644
--- a/nix/libstore/build.cc
+++ b/nix/libstore/build.cc
@@ -1034,8 +1034,10 @@ void DerivationGoal::haveDerivation()
 
     /* We are first going to try to create the invalid output paths
        through substitutes.  If that doesn't work, we'll build
-       them. */
-    if (settings.useSubstitutes && substitutesAllowed(drv))
+       them.  Always enable substitutes for fixed-output derivations to
+       protect against disappearing files and in-place modifications on
+       upstream sites.  */
+    if ((fixedOutput || settings.useSubstitutes) && substitutesAllowed(drv))
         foreach (PathSet::iterator, i, invalidOutputs)
             addWaitee(worker.makeSubstitutionGoal(*i, buildMode == bmRepair));