This article investigates process integration in a direct methanol fuel-cell system from the points of view of controllability, efficiency, and safety. The two cooling and separation lines of anodic and cathodic effluent from the cell stack of a reference system are integrated into a single one. The potential for process integration is measured quantitatively, determining how much the heat exchangers need to be oversized in the reference system, and qualitatively, considering the expected benefits of a more integrated system. The control layout of the reference system is redesigned for the integrated system, without significant loss in dynamic and steady-state performance. A significant disadvantage of the integrated layout is the increased loss of unreacted methanol from its exhaust, which reduces efficiency and has safety implications. The integrated system is found most appropriate for small, portable systems for which small size and high energy density are particularly important.