Reducing waste, using byproducts, and natural food additives are important sustainability trends. In this context, the aim of this study was to produce and evaluate a natural food dye, extracted from pumpkin byproducts, powdered and protected by spray-chilling (SC) and a combination of spray-drying and spray-chilling techniques (SDC). The extract was obtained using ethanol as solvent; vegetable fat and gum Arabic were used as carriers. Formulations were prepared with the following core:carrier ratios: SC 20 (20:80), SC 30 (30:70), SC 40 (40:60), SDC 5 (5:95), SDC 10 (10:90), and SDC 15 (15:85). The physicochemical properties of the formed microparticles were characterised, and their storage stability was evaluated over 90 days. The microparticles exhibited colour variation and size increase over time. SDC particles exhibited the highest encapsulation efficiency (95.2–100.8%) and retention of carotenoids in the storage period (60.8–89.7%). Considering the carotenoid content and its stability, the optimal formulation for each process was selected for further analysis. All of the processes and formulations produced spherical particles that were heterogeneous in size. SDC particles exhibited the highest oxidative stability index and the highest carotenoid release in the intestinal phase (32.6%). The use of combined microencapsulation technologies should be considered promising to protect carotenoid compounds.