The diversity and sheer increase in the number of connected Internet of Things (IoT) devices have brought significant concerns associated with storing and protecting a large volume of IoT data. Storage volume requirements and computational costs are continuously rising in the conventional cloud-centric IoT structures. Besides, dependencies of the centralized server solution impose significant trust issues and make it vulnerable to security risks. In this paper, a layer-based distributed data storage design and implementation of a blockchain-enabled large-scale IoT system are proposed. It has been developed to mitigate the above-mentioned challenges by using the Hyperledger Fabric (HLF) platform for distributed ledger solutions. The need for a centralized server and a third-party auditor was eliminated by leveraging HLF peers performing transaction verifications and records audits in a big data system with the help of blockchain technology. The HLF blockchain facilitates storing the lightweight verification tags on the blockchain ledger. In contrast, the actual metadata are stored in the off-chain big data system to reduce the communication overheads and enhance data integrity. Additionally, a prototype has been implemented on embedded hardware showing the feasibility of deploying the proposed solution in IoT edge computing and big data ecosystems. Finally, experiments have been conducted to evaluate the performance of the proposed scheme in terms of its throughput, latency, communication, and computation costs. The obtained results have indicated the feasibility of the proposed solution to retrieve and store the provenance of large-scale IoT data within the Big Data ecosystem using the HLF blockchain. The experimental results show the throughput of about 600 transactions, 500 ms average response time, about 2–3% of the CPU consumption at the peer process and approximately 10–20% at the client node. The minimum latency remained below 1 s however, there is an increase in the maximum latency when the sending rate reached around 200 transactions per second (TPS).