diff --git a/src/libstore/local-store.cc b/src/libstore/local-store.cc
index 49991e38a..ce0206145 100644
--- a/src/libstore/local-store.cc
+++ b/src/libstore/local-store.cc
@@ -62,6 +62,8 @@ struct LocalStore::State::Stmts {
     SQLiteStmt QueryReferences;
     SQLiteStmt QueryReferrers;
     SQLiteStmt InvalidatePath;
+    SQLiteStmt InvalidatePhantomReferrers;
+    SQLiteStmt QueryPhantomReferrers;
     SQLiteStmt AddDerivationOutput;
     SQLiteStmt RegisterRealisedOutput;
     SQLiteStmt UpdateRealisedOutput;
@@ -384,6 +386,10 @@ LocalStore::LocalStore(const Params & params)
         "select path from Refs join ValidPaths on referrer = id where reference = (select id from ValidPaths where path = ?);");
     state->stmts->InvalidatePath.create(state->db,
         "delete from ValidPaths where path = ?;");
+    state->stmts->InvalidatePhantomReferrers.create(state->db,
+        "delete from Refs where referrer IN (select referrer from Refs left join ValidPaths on referrer = id where reference = (select id from ValidPaths where path = ?));");
+    state->stmts->QueryPhantomReferrers.create(state->db,
+        "select referrer from Refs left join ValidPaths on referrer = id where reference = (select id from ValidPaths where path = ?);");
     state->stmts->AddDerivationOutput.create(state->db,
         "insert or replace into DerivationOutputs (drv, id, path) values (?, ?, ?);");
     state->stmts->QueryValidDerivers.create(state->db,
@@ -1522,6 +1528,18 @@ void LocalStore::invalidatePathChecked(const StorePath & path)
             if (!referrers.empty())
                 throw PathInUse("cannot delete path '%s' because it is in use by %s",
                     printStorePath(path), showPaths(referrers));
+
+            // Note: `queryReferrers` will only return *valid* referrers.
+            // i.e. referrer for which there is a *ValidPath* row in the SQLite database.
+            // In the unfortunate situation where a valid path is removed but its corresponding `Refs` are not removed (*), we better just invalidate all these phantom referrers,
+            // otherwise we will create a foreign key violation when we actually try to invalidate paths.
+            //
+            // (*) : yes, there's a "ON DELETE CASCADE" on the referrer foreign key.
+            // Unfortunately, in practice, it doesn't ensure integrity over large SQLite databases.
+            if (hasPhantomReferrers(*state, path)) {
+                warn("'%s' has phantom referrers (disappeared referrers from the valid path table)", printStorePath(path));
+                invalidatePhantomReferrers(*state, path);
+            }
             invalidatePath(*state, path);
         }
 
@@ -1529,6 +1547,24 @@ void LocalStore::invalidatePathChecked(const StorePath & path)
     });
 }
 
+bool LocalStore::hasPhantomReferrers(State & state, const StorePath & path)
+{
+    return retrySQLite<bool>([&]() -> bool {
+        debug("checking for phantom referrers for '%s'", printStorePath(path));
+        auto useQueryPhantomReferrers(state.stmts->QueryPhantomReferrers.use()(printStorePath(path)));
+
+        return useQueryPhantomReferrers.next();
+    });
+}
+
+void LocalStore::invalidatePhantomReferrers(State & state, const StorePath & path)
+{
+    retrySQLite<void>([&]() {
+        debug("invalidating phantom referrers to '%s'", printStorePath(path));
+        state.stmts->InvalidatePhantomReferrers.use()(printStorePath(path)).exec();
+    });
+}
+
 
 bool LocalStore::verifyStore(bool checkContents, RepairFlag repair)
 {
diff --git a/src/libstore/local-store.hh b/src/libstore/local-store.hh
index 1913aa192..945c94688 100644
--- a/src/libstore/local-store.hh
+++ b/src/libstore/local-store.hh
@@ -322,6 +322,14 @@ private:
      * Delete a path from the Nix store.
      */
     void invalidatePathChecked(const StorePath & path);
+    /**
+     * Check if there's phantom referrers for a certain path in the Nix SQLite database
+     */
+    bool hasPhantomReferrers(State & state, const StorePath & path);
+    /**
+     * Invalidate all phantom referrers from the Nix SQLite database.
+     */
+    void invalidatePhantomReferrers(State & state, const StorePath & path);
 
     void verifyPath(const StorePath & path, const StorePathSet & store,
         StorePathSet & done, StorePathSet & validPaths, RepairFlag repair, bool & errors);
diff --git a/tests/functional/common/vars-and-functions.sh.in b/tests/functional/common/vars-and-functions.sh.in
index 451cf5383..f015b7eb3 100644
--- a/tests/functional/common/vars-and-functions.sh.in
+++ b/tests/functional/common/vars-and-functions.sh.in
@@ -16,6 +16,7 @@ fi
 export NIX_LOCALSTATE_DIR=$TEST_ROOT/var
 export NIX_LOG_DIR=$TEST_ROOT/var/log/nix
 export NIX_STATE_DIR=$TEST_ROOT/var/nix
+export NIX_SQLITE_DATABASE=$NIX_STATE_DIR/db/db.sqlite
 export NIX_CONF_DIR=$TEST_ROOT/etc
 export NIX_DAEMON_SOCKET_PATH=$TEST_ROOT/dSocket
 unset NIX_USER_CONF_FILES
@@ -164,6 +165,10 @@ requireDaemonNewerThan () {
     isDaemonNewer "$1" || skipTest "Daemon is too old"
 }
 
+requireSqliteDatabase() {
+    [[ -f "$NIX_SQLITE_DATABASE" ]] || skipTest "SQLite database is not used for this store implementation"
+}
+
 canUseSandbox() {
     [[ ${_canUseSandbox-} ]]
 }
diff --git a/tests/functional/meson.build b/tests/functional/meson.build
index f56ced48d..aeb8aa739 100644
--- a/tests/functional/meson.build
+++ b/tests/functional/meson.build
@@ -76,6 +76,7 @@ functional_tests_scripts = [
   'flakes/flake-registry.sh',
   'flakes/subdir-flake.sh',
   'gc.sh',
+  'phantom-referrers-gc.sh',
   'nix-collect-garbage-d.sh',
   'nix-collect-garbage-dry-run.sh',
   'remote-store.sh',
diff --git a/tests/functional/phantom-referrers-gc.sh b/tests/functional/phantom-referrers-gc.sh
new file mode 100644
index 000000000..72d54d91f
--- /dev/null
+++ b/tests/functional/phantom-referrers-gc.sh
@@ -0,0 +1,62 @@
+source common.sh
+
+startDaemon
+
+requireDaemonNewerThan "2.92.0"
+requireSqliteDatabase
+
+clearStore
+
+depOutPath=$(nix-build --no-out-link -E '
+  with import ./config.nix;
+
+  mkDerivation {
+    name = "phantom";
+    outputs = [ "out" ];
+    buildCommand = "
+      echo i will become a phantom soon > $out
+    ";
+  }
+')
+
+finalOutPath=$(nix-build --no-out-link -E '
+  with import ./config.nix;
+
+  let dep = mkDerivation {
+    name = "phantom";
+    outputs = [ "out" ];
+    buildCommand = "
+      echo i will become a phantom soon > $out
+    ";
+  }; in
+
+  mkDerivation {
+    name = "phantom-gc";
+    outputs = [ "out" ];
+    buildCommand = "
+      echo UNUSED: ${dep} > $out
+    ";
+  }
+')
+
+echo "displaying all valid paths"
+sqlite3 "$NIX_SQLITE_DATABASE" <<EOF
+  select * from validpaths;
+EOF
+
+
+echo "displaying the relevant IDs..."
+sqlite3 "$NIX_SQLITE_DATABASE" <<EOF
+  select r.referrer, r.reference from Refs r join ValidPaths vp on r.referrer = vp.id where path = '$finalOutPath';
+EOF
+
+echo "corrupting the SQLite database manually..."
+sqlite3 "$NIX_SQLITE_DATABASE" <<EOF
+  pragma foreign_keys = off;
+  delete from ValidPaths where path = '$finalOutPath';
+  select * from Refs;
+EOF
+
+restartDaemon
+# expect this to work and maybe warn about phantom referrers
+expectStderr 0 nix-collect-garbage -vvvv | grepQuiet 'phantom referrers'