This paper proposes a novel Blockchain-based indoor navigation system that combines a foot-mounted dual-inertial measurement unit (IMU) setup and a zero-velocity update (ZUPT) algorithm for secure and accurate indoor navigation in GNSS-denied environments. The system estimates the user’s position and orientation by fusing the data from two IMUs using an extended Kalman filter (EKF). The ZUPT algorithm is employed to detect and correct the error introduced by sensor drift during zero-velocity intervals, thus enhancing the accuracy of the position estimate. The proposed Low SWaP-C blockchain-based decentralized architecture ensures the security and trustworthiness of the system by providing an immutable and distributed ledger to store and verify the sensor data and navigation solutions. The proposed system is suitable for various indoor navigation applications, including autonomous vehicles, robots, and human tracking. The experimental results provide clear and compelling evidence of the effectiveness of the proposed system in ensuring the integrity, privacy, and security of navigation data through the utilization of blockchain technology. The system exhibits an impressive ability to process more than 680 transactions per second within the Hyperledger-Fabric framework. Furthermore, it demonstrates exceptional accuracy and robustness, with a mean RMSE error of 1.2 m and a peak RMSE of 3.2 during a 20 min test. By eliminating the reliance on external signals or infrastructure, the system offers an innovative, practical, and secure solution for indoor navigation in environments where GNSS signals are unavailable.