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Internet of things grew swiftly and many services, software, sensors-embedded electronic devices and related protocols were developed and still in progress with full swing. Internet of things enabling physically existing things to see, hear, think and perform a notable task by allowing them to talk to each other and share useful information while making decision and caring-on/out their important tasks. Internet of things is greatly promoted by wireless sensor network as it becomes a perpetual layer for it. Wireless sensor network works as a base-stone for most of the Internet of things applications. There are severe general and specific threats and technical challenges to Internet of things–based sensor networks which must overcome to ensure adaptation and diffusion of it. Most of the limitations of wireless sensor networks are due to its resource constraint objects nature. The specified open research challenges in Internet of things–based sensor network are power consumption, network lifespan, network throughput, routing and network security. To overcome aforementioned problems, this work aimed to prolong network lifetime, improve throughput, decrease packet latency/packet loss and further improvise in encountering malicious nodes. To further tune the network lifetime in terms of energy, wireless harvesting energy is suggested in proposed three-layer cluster-based wireless sensor network routing protocol. The proposed mechanism is a three-tier clustering technique with implanted security mechanism to encounter malicious activities of sensor nodes and to slant them into blacklist. It is a centred-based clustering protocol, where selection of cluster head and grid head is carried out by sink node based on the value of its cost function. Moreover, hardware-based link quality estimators are used to check link effectiveness and to further improve routing efficiency. At the end, excessive experiments have been carried out to check efficacy of the proposed protocol. It outperforms most of its counterpart protocols such as fuzzy logic–based unequal clustering and ant colony optimization–based routing hybrid, Artificial Bee Colony-SD, enhanced three-layer hybrid clustering mechanism and energy aware multi-hop routing in terms of network lifetime, network throughput, average energy consumption and packet latency.