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Hydrothermal treatment (HTT) offers the potential to upgrade low-value biomass such as digestate (DG) or forest residue (FR) by producing solids and liquids for material use or energetic utilization. In this study, microwave-assisted HTT experiments with DG and FR as feedstocks were executed at different temperatures (130, 150, 170 °C) and with different holding times (30, 60, 90 min) to determine the influences on product properties (ash and elemental concentrations, calorific values and chemical compounds). In general, DG and FR reacted differently to HTT. For the DG solids, for instance, the ash concentration was reduced to 8.68%DM at 130 °C (initially 27.67%DM), and the higher heating value increased from 16.55 MJ/kgDM to 20.82 MJ/kgDM at 170 °C, while the FR solids were affected only marginally. Elements with importance for emissions in combustion were leached out in both HTT solids. The DG and FR liquids contained different chemical compounds, and the temperature or holding time affected their formation. Depending on the designated application of HTT, less severe conditions can deliver better results. It was demonstrated that different low-temperature HTT conditions already induce strong changes in the product qualities of DG and FR. Optimized interactions between process parameters (temperature, holding time and feedstock) might lead to better cost–benefit effects in HTT.