The formation of humins is one drawback of biomass valorization (e.g., hemicellulosic fraction) toward platform chemicals and fuels. Furanic compounds including 5-hydroxymethylfurfural (HMF) and 5-methoxymethylfurfural (MMF) can be extracted from humins and valorized. Unlike HMF, reactions with MMF have not been widely studied. In this work, MMF was extracted from humins aiming to its hydrogenation in continuous flow. Based on success from literature studies with HMF hydrogenation, 5% Ru/C and 5% Pd/C catalysts were employed, and both have demonstrated excellent conversion of MMF toward hydrogenation products (100%), with an interesting selectivity switch depending on reaction conditions. Ru-based catalysts were more prone to deactivation as compared to Pd catalysts and were extremely stable after a few hours on stream under the investigated reaction conditions. A reaction mechanism was proposed for MMF hydrogenation.