The extraction of bioactive compounds from fruits, such as lemon, has gained relevance because these compounds have beneficial properties for health, such as antioxidant and anticancer properties; however, the extraction method can significantly affect these properties. High hydrostatic pressure and ultrasound, as emerging extraction methods, constitute an alternative to conventional extraction, improving extractability and obtaining extracts rich in bioactive compounds. Therefore, lemon extracts (LEs) were obtained by conventional (orbital shaking), ultrasound-assisted, and high-hydrostatic-pressure extraction. Extracts were then microencapsulated with maltodextrin at 10% (M10), 20% (M20), and 30% (M30). The impact of microencapsulation on LEs physicochemical properties, phenolics (TPC), flavonoids (TFC) and relative bio-accessibility (RB) was evaluated. M30 promoted a higher microencapsulation efficiency for TPC and TFC, and a longer time required for microcapsules to dissolve in water, as moisture content, water activity and hygroscopicity decreased. The RBs of TPC and TFC were higher in microcapsules with M30, and lower when conventional extraction was used. The data suggest that microencapsulated LE is promising as it protects the bioactivity of phenolic compounds. In addition, this freeze-dried product can be utilized as a functional ingredient for food or supplement formulations.