This work presents an experimental holistic approach for the design of a continuous catalytic conversion process of carbohydrates derived from waste biomass to 5-hydroxymethylfurfural (5-HMF) using a tin-doped active carbon catalyst. In this report, apple biomass waste is used as a model component as feed. This work demonstrates the synergistic benefit of the catalyst performance integrated with various process steps to increase 5-HMF yield by using a holistic approach instead of considering the catalyst as an isolated piece within the process. A detailed process layout is presented, and process parameters have been investigated systematically to optimize the continuous catalytic conversion of biomass. The extraction of components such as enzymes from the apple pomace with 20 v % n-butanol after milling was found to be an essential pretreatment procedure for stable catalytic performance substantially improving 5-HMF yield. The optimum catalytic reaction conditions with respect to temperature, contact time, and catalyst regeneration were investigated as well as the feasibility to apply downstream membrane filtration to clean the product stream by removing humins. To increase process efficiency, addition of hydrolyzed pulp filter cake to the reactant feed was investigated. The spent Sn-doped carbon catalysts were analyzed using various techniques, such as N2 physisorption, X-ray fluorescence, X-ray diffraction, ammonia-temperature-programmed desorption, and thermogravimetric analysis.