The methodology of processing biomass for the production of fuels and chemicals has been well established; however, these processes are often not economical due to the high cost of materials and low selectivity. In order to more efficiently use the raw materials, and to decrease processing (and developing) time, it is necessary to consider novel synthesis routes and/or novel process technologies for biomass valorization. The use of micro-/millireactor technology for this purpose is still under investigation. This review introduces relevant processes for the conversion of biomolecules into the industrially valuable products developed (or under development) in a microreactor. The processes with the enzyme- and metal-based catalysts are considered and carbohydrates, amino acids, and their derivatives as starting materials for processing in microreactors are reviewed as well. Also, we discuss main motivations, achievements, and current challenges when using microreactor technology, and the status of a holistic process design approach in relevant fields. We suggest that although there are individual examples reported on sustainable process design including microreactor technology, the systematic approach is still missing.