In this paper, we address the problem of compatibility between digital signature schemes and in-network aggregation approaches. In the IoT world, the gateways alter the signed network flows when performing in-network aggregation. Therefore, existing conventional approaches are not suitable for verifying the authenticity of the original flows. This raises the need for energy-effective and secure schemes that enable the destination to validate aggregated network flows. In this regard, a lightweight homomorphic signature scheme is proposed which supports the implementation of aggregation procedures without affecting the verification process. We demonstrate the unforgeability and the privacy of our scheme. We also perform an analytical study of its energy-efficiency. The results suggest that the proposed scheme considerably decreases the processing overhead of the existing set-homomorphic signature schemes. Moreover, it does not add any communication overhead to traditional (non-homomorphic) signature schemes. This, in turn, improves the energy consumption by 30% compared to existing homomorphic signature techniques.