While the large-scale Internet of Things (IoT) makes many new applications feasible, like Smart Cities, IoT also brings new concerns on data reliability, security, and privacy. The rapid evolution in blockchain technologies, which relied on a decentralized, immutable and distributed ledger system for transaction data auditing, provides a prospective solution to address the issues in IoT. The blockchain and smart contract enabled security mechanism for IoT applications have attracted increasing interests from both academia and industry. However, integrating cryptocurrency-oriented blockchain technologies into IoT systems meets tremendous challenges on scalability, storage capacity, security, and privacy. Particularly, the performance of blockchain networks significantly relies on the performance of consensus mechanisms, e.g., in terms of data confidentiality, transaction throughput, and network scalability. In this chapter, given an in-depth review of state-of-the-art blockchain networks, the key matrix of designing consensus mechanism for IoT networks are identified in terms of throughput, scalability, and security. To demonstrate a case study on designing scalable, lightweight blockchain protocols for IoT systems, a Microchain framework is introduced and a proof-of-concept prototype is implemented in a physical network environment. The experimental results verify the feasibility of integrating the Microchain into IoT systems.