This research presents the microencapsulation and conservation of antioxidants of broccoli juice processed by spray drying, and proposes the use of a by-product as a technological application. Broccoli juice (BJ) extracted from two sources, stalks and florets, was spray-dried employing maltodextrin (MX) as a carrier agent at concentrations of 5, 7.5, and 10%, and inlet temperatures of 150 and 220 °C. The total phenolic content (TPC), and antioxidant activity (AA) of the BJ-MX powders were determined together with the physicochemical characteristics, including particle morphology, microstructure, and thermal properties. Based on the TPC and AA, the optimal processing conditions found were 5% of MX and a drying temperature of 220 °C. However, the florets showed higher TPC, while stalks presented higher AA under those processing conditions. The particles exhibited micrometric sizes and a mixture of spherical-shape particles and pseudo-spherical particles. The diffractograms indicated an amorphous microstructure in all samples. The glass transition temperature (Tg) was determined in the range of 50 °C for the samples dried at 150 °C and 55 °C for those dried at 220 °C. This suggested that powders might be stored at temperatures below the Tg without presenting any loss of antioxidants.