The increasing demand for natural dyes, such as betalains, particularly betaxanthins, arises from their remarkable bioactive properties. However, the industrial application of these compounds is limited by their low stability in response to pH, light, and temperature variations. Microencapsulation by freeze-drying presents a promising strategy to enhance the stability and functionality of betaxanthins. This study aimed to encapsulate betaxanthins from yellow pitaya (Selenecereus megalanthus) peel, using maltodextrin (MD) with a dextrose equivalent of 10 and animal-based proteins as wall materials. The extraction of betaxanthins was performed using 60% ethanol (v/v) at room temperature (25 ± 1 °C) for 20 minutes, in a 1:1 ratio (w/v, peel: solution). The betaxanthin-rich extract was used to prepare five formulations utilizing maltodextrin (15%, 14.5%, or 14%), combined with myofibrillar proteins from mechanically separated chicken meat (MPC, 0%, 0.5%, or 1%) or with whey protein concentrate (WPC, 0%, 0.5%, or 1%). The formulations were subjected to rheological analysis and then freeze-dried, resulting in microparticles that were evaluated for water activity, instrumental color, yield, encapsulation retention, betaxanthin content, and phenolic compounds. The rheological analysis revealed that the solutions exhibited a pseudoplastic non-Newtonian fluid profile (n<1). The addition of animal-derived proteins significantly reduced the water activity of the produced microparticles, particularly in the formulations containing WPC (p<0.05). The microparticles containing WPC demonstrated enhanced physicochemical properties, with the formulation composed of 14% MD and 1% WPC showing high levels of betaxanthin (2.65 ± 0.03 mg/g) and phenolic compounds (331.97 ± 11.78 mg of gallic acid/100 g), as well as high encapsulation retention of betaxanthin (84.86 ± 0.92%) and freeze-drying yield (75.94 ± 4.18%). All microparticles exhibited a uniform yellow coloration (p>0.05), indicating good pigment retention. In conclusion, freeze-drying microencapsulation combining MD and WPC effectively retained betaxanthins, enabling their application as a bioactive natural dye.