Phenolic compounds that are present in pineapple by-products offer many health benefits to the consumer; however, they are unstable to many environmental factors. For this reason, encapsulation is ideal for preserving their beneficial effects. In this work, extracts were obtained by the combined method of solid-state fermentation with Rhizopus oryzae and ultrasound. After this process, the encapsulation process was performed by ionotropic gelation using corn starch, sodium alginate, and Weissella confusa exopolysaccharide as wall material. The encapsulates produced presented a moisture content between 7.10 and 10.45% (w.b), a solubility of 53.06 ± 0.54%, and a wettability of 31.46 ± 2.02 s. The total phenolic content (TPC), antioxidant capacity of DPPH, and ABTS of the encapsulates were also determined, finding 232.55 ± 2.07 mg GAE/g d.m for TPC, 45.64 ± 0.9 µm Trolox/mg GAE for DPPH, and 51.69 ± 1.08 µm Trolox/mg GAE for ABTS. Additionally, ultrahigh performance liquid chromatography (UHPLC) analysis allowed us to identify and quantify six bioactive compounds: rosmarinic acid, caffeic acid, p-coumaric acid, ferulic acid, gallic acid, and quercetin. According to the above, using ionotropic gelation, it was possible to obtain microencapsulates containing bioactive compounds from pineapple peel extracts, which may have applications in the development of functional foods.