In safety-critical and high-integrity computing, it is important to guarantee both performance and time-predictability of I/O operations. However, with the continued growth of hardware and architectural complexity, satisfying such real-time requirements has become increasingly challenging because of complex I/O transaction paths and extensive hardware contention. This paper proposes a systematic framework with a novel I/O controller and a reconfigurable NoC, effectively optimising I/O transaction paths to encounter reduced contention. Moreover, we present a theoretical model and optimisation process to further improve real-time performance. The evaluations show that our approach outperforms state-of-the-art I/O processing techniques on a range of metrics.