diff --git a/radicle-node/src/service.rs b/radicle-node/src/service.rs
index fad9cfa54..c7069ab7c 100644
--- a/radicle-node/src/service.rs
+++ b/radicle-node/src/service.rs
@@ -555,6 +555,19 @@ where
         let nid = self.node_id();
         self.started_at = Some(time);
 
+        // Populate refs database. This is only useful as part of the upgrade process for nodes
+        // that have been online since before the refs database was created.
+        match self.db.refs().count() {
+            Ok(0) => {
+                info!(target: "service", "Empty refs database, populating from storage..");
+                if let Err(e) = self.db.refs_mut().populate(&self.storage) {
+                    error!(target: "service", "Failed to populate refs database: {e}");
+                }
+            }
+            Ok(n) => debug!(target: "service", "Refs database has {n} cached references"),
+            Err(e) => error!(target: "service", "Error checking refs database: {e}"),
+        }
+
         // Ensure that our local node is in our address database.
         self.db
             .addresses_mut()
diff --git a/scripts/clear-refs-db.sh b/scripts/clear-refs-db.sh
new file mode 100755
index 000000000..ff70af01b
--- /dev/null
+++ b/scripts/clear-refs-db.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+set -e
+
+DB="$(rad path)/node/node.db"
+
+if command -v sqlite3 >/dev/null 2>&1; then
+  if [ -f "$DB" ]; then
+    echo -n "Clearing 'refs' table from $DB.. "
+    sqlite3 $DB "DELETE FROM refs;"
+    echo "done."
+  else
+    echo "fatal: database file does not exist"
+    exit 1
+  fi
+else
+  echo "fatal: sqlite3 is not installed"
+  exit 1
+fi