Wireless sensor networks (WSNs) comprise a large number of tiny sensing nodes, which are battery-powered with limited energy. An energy-efficient routing protocol is of utmost importance to prolong the network lifetime. Clustering is the most common technique to balance energy consumption among all nodes, while minimizing traffic and overhead during the data transmission phases. In this paper, a Multi-Objective nature-inspired algorithm based on Shuffled frog-leaping algorithm and Firefly Algorithm (named MOSFA) as an adaptive application-specific clustering-based multi-hop routing protocol for WSNs is proposed. MOSFA’s multi-objective function regards different criteria (e.g., inter- and intra-cluster distances, the residual energy of nodes, distances from the sink, overlap, and load of clusters) to select appropriate cluster heads at each round. Moreover, another multi-objective function is proposed to select the forwarder nodes in the routing phase. The controllable parameters of MOSFA in both clustering and multi-hop phases can be adaptively tuned to achieve the best performance based on the network requirements according to the specific application. Simulation results demonstrate average lifetime improvements of 182%, 68%, 30%, and 28% when compared with LEACH, ERA, SIF, and FSFLA, respectively, in different network scenarios.