In today’s world, a major challenge is to conserve and make optimal use of energy. This is a critical matter in wireless sensor networks due to their wide application in different areas. More importantly, scant attention has been paid to the use of node energy for certain applications in such networks. This study used the Shuffled Frog Leaping Algorithm (SFLA) to propose a Fuzzy Multi-hop clustering protocol (FMSFLA). The SFLA is used for automated configuration and optimization of the rule-base table in a fuzzy inference system and five adjustable parameters in two phases, i.e. Cluster Head (CH) selection and parent selection, based on application features. The proposed protocol (FMSFLA) considers effective parameters including energy, distance from the base station (BS), the number of neighboring nodes, real node distance from the BS, mean route load, delay, overlap, and the problem of hot spots, to achieve the best application-based performance. The FMSFLA includes rounds, in each round the phases of CH selection, parent selection, cluster formation, and steady state are performed. In the CH selection phase, CHs are selected from candidate nodes based on the fuzzy output and energy threshold (i.e. a control parameter) with respect to the overlap rate of adjacent CHs. In our protocol, the parent selection phase began by determining the levels of CHs in the network. At the end of this phase, the parent of each CH is determined on the basis of the greatest fuzzy output based on application. In the cluster formation phase, the clusters are formed on the basis of the determined CHs. Finally, the information received by CHs is sent through their parents to the BS in the steady state phase. The FMSFLA is evaluated against the LEACH, LEACH-EP, LEACH-FL, ASLPR, SIF, and ERA protocols in terms of the number of alive nodes, received packets, and cluster heads in addition to their appropriate distribution rates and other parameters pertaining to the network lifetime and protocol scalability using three application-oriented scenarios. According to the simulation results, the FMSFLA functioned far better than the other protocols in all scenarios with respect to goals and application features.