The encapsulation efficiency (EE%) and structural changes within the Anthraquinones-encapsulated casein micelles (CM) powders were evaluated in this study. For this purpose, the anthraquinone powder extracted from Aloevera, its freeze-dried powder (FDP) and whole leaf Aloe vera gel (WLAG) has been encapsulated in CM through ultrasonication prior to spray dying to produce nanocapsules: CM encapsulated anthraquinone powder (CMAQP), CM encapsulated freeze-dried powder (CMFDP) and CM encapsulated Whole leaf aloe vera gel (CMWLAG). Based on the pH of the solution before drying, CMAQP had the highest EE% following spray drying. However, due to air-interface-related dehydration stresses, SD resulted in a slight decrease in the EE% of anthraquinones (aloin, aloe-emodin, and rhein) in CMAQP. Meanwhile, a significant increase in EE% of CMFDP was observed compared to the aqueous state. According to SEM findings, the particle size of CMAQP was 2.39 µm and ξ-potential of ~−17mV. The CMFDP had a rough fractal surface with large particle sizes and potential of 3.49 µm and ~−11mV respectively. CM deformed, having the least EE% and lowest ξ-potential (−4.5 mV). Spray drying enhances melanoidin formation in CMWLAG, as evidenced by the highest chroma values. The results suggested that EE%, stability, and degree of Maillard reaction are closely linked to the type of anthraquinone encapsulated, the pH of the solution, and the nanostructure of casein micelles during spray drying.