The present study investigates and discusses the role of sample pretreatment and reactor design during hydrothermal carbonization (HTC) of agro-waste. Results highlighted the role of sample pre-drying and reactor design as key factors determining the process reaction pathways and thus products distribution and properties. Pineapple, orange and tangerine peel waste, with or without drying pretreatment, were carbonized in a 50 (not stirred) and 500 (stirred) mL batch stainless steel reactors at three different operating temperatures (180, 220, 250 °C). HTC solid residues were characterized in terms of proximate and elemental analysis and higher heating values while liquid phases were characterized in terms of pH and total organic carbon content. When comparing wet to dried samples, the former showed a significant increase of gas yield (about 20 wt%), which has grown more rapidly with increasing reaction temperature. Pre-treated samples (subjected to drying and water content reintegration before reaction) showed an almost constant hydrochar mass yield with increasing reaction temperature and higher rate of decomposition at milder temperatures when compared to corresponding wet samples. Higher reactivity of “dry” samples and constant hydrochar mass yields with temperature were related to higher degree of secondary char production via condensation and re-polymerization reactions of organics from the liquid phase. Reactor stirring also significantly influenced the HTC residues distribution, leading to greater gas production and lower hydrochar mass yields, compared to 50 mL not stirred reactor.