This paper presents the incorporation of process flexibility into a methanol synthesis loop operating under catalyst deactivation. A design methodology is discussed with regard to catalyst deactivation, and some limitations are identified. In the current flexibility study the size of the reactor and recycle ratio have been fixed. Attempts to maintain methanol production at the rates observed with fresh catalyst included increased pressure, increased make up gas flow rate, and the injection of carbon dioxide into the make up gas at optimized inlet temperature. In order to provide flexibility and produce a design compatible with increased production rates, the effect of interrelating equipment had to be considered. As a result of catalyst deactivation, an increased flow rate is necessary and the altered process streams entering the preheater disturb the reactor inlet temperature. These issues should be considered in the design stage and may be resolved by the flexible designs presented.