diff --git a/src/hydra-queue-runner/builder.cc b/src/hydra-queue-runner/builder.cc
index 983ebfec..8a636b17 100644
--- a/src/hydra-queue-runner/builder.cc
+++ b/src/hydra-queue-runner/builder.cc
@@ -263,6 +263,9 @@ State::StepResult State::doBuildStep(nix::ref<Store> destStore,
 
         assert(stepNr);
 
+        for (auto & path : step->drv.outputPaths())
+            writeFile(rootsDir + "/" + baseNameOf(path), "");
+
         /* Register success in the database for all Build objects that
            have this step as the top-level step. Since the queue
            monitor thread may be creating new referring Builds
diff --git a/src/hydra-queue-runner/hydra-queue-runner.cc b/src/hydra-queue-runner/hydra-queue-runner.cc
index 9c56beda..4d0ec169 100644
--- a/src/hydra-queue-runner/hydra-queue-runner.cc
+++ b/src/hydra-queue-runner/hydra-queue-runner.cc
@@ -87,6 +87,7 @@ State::State()
     , maxOutputSize(config->getIntOption("max_output_size", 2ULL << 30))
     , maxLogSize(config->getIntOption("max_log_size", 64ULL << 20))
     , uploadLogsToBinaryCache(config->getBoolOption("upload_logs_to_binary_cache", false))
+    , rootsDir(config->getStrOption("gc_roots_dir", fmt("%s/gcroots/per-user/%s/hydra-roots", settings.nixStateDir, getEnv("USER"))))
 {
     debug("using %d bytes for the NAR buffer", memoryTokens.capacity());
 
diff --git a/src/hydra-queue-runner/queue-monitor.cc b/src/hydra-queue-runner/queue-monitor.cc
index 895363bc..85d8f626 100644
--- a/src/hydra-queue-runner/queue-monitor.cc
+++ b/src/hydra-queue-runner/queue-monitor.cc
@@ -221,6 +221,9 @@ bool State::getQueuedBuilds(Connection & conn,
             Derivation drv = readDerivation(build->drvPath);
             BuildOutput res = getBuildOutputCached(conn, destStore, drv);
 
+            for (auto & path : drv.outputPaths())
+                writeFile(rootsDir + "/" + baseNameOf(path), "");
+
             {
             auto mc = startDbUpdate();
             pqxx::work txn(conn);
diff --git a/src/hydra-queue-runner/state.hh b/src/hydra-queue-runner/state.hh
index d8dc11f7..f5ba641e 100644
--- a/src/hydra-queue-runner/state.hh
+++ b/src/hydra-queue-runner/state.hh
@@ -436,6 +436,11 @@ private:
 
     bool uploadLogsToBinaryCache;
 
+    /* Where to store GC roots. Defaults to
+       /nix/var/nix/gcroots/per-user/$USER/hydra-roots, overridable
+       via gc_roots_dir. */
+    nix::Path rootsDir;
+
 public:
     State();