Higher-order multi-input multi-output systems pose challenges in terms of stability and control performance due to increased complexity and interactions between multiple subsystems. Hence, this research work proposes a novel comprehensive approach to design a decentralised fractional order control strategy for higher-order systems using tree seed algorithm. The design focuses on enhancing control performance by imposing constraints on performance indices – the integral of absolute error and closed-loop amplitude ratio. Further, this work incorporates stability analysis through the singular values of the sensitivity function. The proposed decentralised fractional-order proportional-integral-derivative (FOPID) controller parameters are optimised using the tree seed algorithm. Besides, the stability is examined using the singular values of the sensitivity function. The tree seed algorithm explores the parameter space and converges to optimal controller settings that satisfy the imposed constraints by ensuring system stability. Simulation studies are conducted on various higher-order systems to analyse the proposed approach. The findings demonstrate that the decentralised control with tree seed algorithm-based FOPID controller achieves improved control performance by reducing the loop interactions among subsystems with enhanced stability. Furthermore, robustness is ensured by considering output uncertainty and parameter variations.