Minerals are essential for a number of vital health processes. Recommended Daily Intake (RDI) values have been established and the deficiency of certain minerals is considered a serious public health issue. Plant-based beverage (PBB) is a global trend as an alternative to milk, juices, and other drinks. This product is generally low in selenium (Se), a trace element that is considered essential for health. In this context, fortifying PBB with Se may provide health benefits, such as antioxidant protection, improvement of the immune system and reduced risk of chronic diseases. The aim of this study was to estimate the in vitro bioaccessibility of Se in commercial PBBs (almonds, rice and soybean) fortified with isolated salts and encapsulated microparticles of sodium selenate, obtained through combined methods (spray-chilling and spray-drying). The PBBs considered to have low Se levels (total Se < 4.0 µg/kg) were purchased commercially and fortified with Se levels equivalent to the RDI (55 µg/day). The acid digestion method assisted by ultrasound and ICP-MS was used to quantify Se, while the static in vitro digestion method (INFOGEST 2.0) was employed to assess the bioaccessibility percentages. The PBBs of almonds, rice, and soybean fortified with isolated salts of sodium selenate had Se-bioaccessibility percentages of 78%, 70% and 68%, respectively, which were lower than those of the beverages fortified with the produced Se-microparticles (83%, 86%, and 84%, respectively). Therefore, the microencapsulation technique of sodium selenate emerges as a tool to enhance the bioaccessibility of Se in PBBs, ensuring a more effective delivery of this nutrient, with potential nutritional benefits for human health.