In direct methanol fuel cells (DMFCs), a dilute methanol and water mixture is generally used and recycled as a fuel to improve the performance and operation time with high fuel efficiency through reduced methanol crossover. Such recycling can, however, allow the continuous accumulation of some reaction intermediates in the circulating loop of dilute methanol during DMFC operation. Therefore, this study examines DMFC contamination sources and the electrochemical influence of recycled methanol fuel by physicochemical analysis of the organic and inorganic (metal) intermediates generated from the DMFC system components. Further, a novel method for mitigating the impact of the reaction intermediates on the performance of DMFC system is proposed.