diff --git a/src/libcmd/installables.cc b/src/libcmd/installables.cc
index 5f263061b..658b415f3 100644
--- a/src/libcmd/installables.cc
+++ b/src/libcmd/installables.cc
@@ -609,10 +609,10 @@ InstallableFlake::getCursors(EvalState & state)
 
 std::shared_ptr<flake::LockedFlake> InstallableFlake::getLockedFlake() const
 {
+    flake::LockFlags lockFlagsApplyConfig = lockFlags;
+    lockFlagsApplyConfig.applyNixConfig = true;
     if (!_lockedFlake) {
-        _lockedFlake = std::make_shared<flake::LockedFlake>(lockFlake(*state, flakeRef, lockFlags));
-        _lockedFlake->flake.config.apply();
-        // FIXME: send new config to the daemon.
+        _lockedFlake = std::make_shared<flake::LockedFlake>(lockFlake(*state, flakeRef, lockFlagsApplyConfig));
     }
     return _lockedFlake;
 }
diff --git a/src/libexpr/flake/flake.cc b/src/libexpr/flake/flake.cc
index 8e6f06949..e266bc36d 100644
--- a/src/libexpr/flake/flake.cc
+++ b/src/libexpr/flake/flake.cc
@@ -298,6 +298,11 @@ LockedFlake lockFlake(
 
     auto flake = getFlake(state, topRef, lockFlags.useRegistries, flakeCache);
 
+    if (lockFlags.applyNixConfig) {
+        flake.config.apply();
+        // FIXME: send new config to the daemon.
+    }
+
     try {
 
         // FIXME: symlink attack
diff --git a/src/libexpr/flake/flake.hh b/src/libexpr/flake/flake.hh
index d17d5e183..4479e95db 100644
--- a/src/libexpr/flake/flake.hh
+++ b/src/libexpr/flake/flake.hh
@@ -104,6 +104,10 @@ struct LockFlags
        references like 'nixpkgs'. */
     bool useRegistries = true;
 
+    /* Whether to apply flake's nixConfig attribute to the configuration */
+
+    bool applyNixConfig = false;
+
     /* Whether mutable flake references (i.e. those without a Git
        revision or similar) without a corresponding lock are
        allowed. Mutable flake references with a lock are always
diff --git a/src/nix/flake.cc b/src/nix/flake.cc
index 64fcfc000..9055b07eb 100644
--- a/src/nix/flake.cc
+++ b/src/nix/flake.cc
@@ -84,6 +84,7 @@ struct CmdFlakeUpdate : FlakeCommand
 
         lockFlags.recreateLockFile = true;
         lockFlags.writeLockFile = true;
+        lockFlags.applyNixConfig = true;
 
         lockFlake();
     }
@@ -114,6 +115,7 @@ struct CmdFlakeLock : FlakeCommand
         settings.tarballTtl = 0;
 
         lockFlags.writeLockFile = true;
+        lockFlags.applyNixConfig = true;
 
         lockFlake();
     }
@@ -270,6 +272,8 @@ struct CmdFlakeCheck : FlakeCommand
         settings.readOnlyMode = !build;
 
         auto state = getEvalState();
+
+        lockFlags.applyNixConfig = true;
         auto flake = lockFlake();
 
         bool hasErrors = false;