Mango (Mangifera indica) peel powder (MP), banana (Musa paradisiaca) peel powder (BP), and yellow tamarillo freeze-dried pulp (Solanum betaceum Cav.) (YT), were selected as raw materials to obtain eight microencapsulates (M1-M8) by spray-drying with maltodextrin (MD) at two air inlet temperatures (130 °C and 180 °C) and with four feed mixture compositions. Their physicochemical characterisation was performed by measuring: pH, soluble solids (°Brix), Aw, and colour CIELAB (L*, a* and b*) parameters. The morphology analysis performed by SEM, determined that the powders showed a regular and spherical microstructure. The qualitative and quantitative carotenoid analyses carried out by HPLC-PDA-APCI/MS methodology, both in the raw materials and microencapsulates, showed that the drying temperature significantly affected the carotenoid content. The major carotenoids in the samples were β-cryptoxanthin C14:0, β-cryptoxanthin C16:0, β-carotene, β-cryptoxanthin C12:0, β-cryptoxanthin, zeaxanthin, and lutein. Among the microencapsulates, M2 and M4 samples (dried at 130 °C) exhibited the highest values of carotenoid content with 1.025 and 1.296 mg β-carotene/100 g sample, respectively. Thermal analyses showed that the powders were stable up to 100 °C. During the storage stability test at 18 °C, the carotenoid content diminished following a first order kinetic, showing the RH strongly influences the stability of microencapsulates.