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Pressure swing adsorption (PSA) technology is used in various applications. PSA is a cost-effective process with the ability to produce high-purity bio-hydrogen (99.99%) with high recovery rates. In this article, a PSA process for the production of bio-hydrogen is proposed; it uses two columns packed with type 5A zeolite, and it has a four-step configuration (adsorption, depressurization, purge, and repressurization) for bio-hydrogen production and regeneration of the beds. The aim of this work is to design and use an active fault-tolerant control (FTC) controller to raise and maintain a stable purity of 0.9999 in molar fraction (99.99%), even with the occurrence of actuator faults. To validate the robustness and performance of the proposed discrete FTC, it has been compared with a discrete PID (proportional–integral–derivative) controller in the presence of actuator faults and trajectory changes. Both controllers achieve to maintain stable purity by reducing the effect of faults; however, the discrete PID controller is not robust to multiple faults since the desired purity is lost and fails to meet international standards to be used as bio-fuel. On the other hand, the FTC scheme reduces the effects of individual and multiple faults by striving to maintain a purity of 0.9999 in molar fraction and complying with international standards to be used as bio-fuel.