Energy efficiency is imperative for enhancing the competitiveness of today's manufacturing. Benchmarking can provide guidance for developing improvement strategies, which requires energy characterisation to determine the current performance, reference points and improvement potentials. However, the present developments in energy benchmarking cannot be applied to a wide range of manufacturing industries. Therefore, this paper presents a generic methodology to characterise the energy efficiency at a factory level and to derive the reference points for benchmarking. A case study is used to demonstrate the validity and applicability of the proposed method.