Cocoa honey, a by-product obtained during the processing of cocoa, is a juice rich in pectin, organic acids, minerals and phenolic compounds with antioxidant properties. Fresh cocoa honey is quickly fermented due to its high content of reducing sugars, such as fructose and glucose, which limits its shelf life. Currently, cocoa honey is only commercialized in frozen form, as logistical challenges prevent the wide distribution or export of this by-product for applications in the market of sweets, jellies, beverages, confectionery, and nutraceutical foods among others. Spray-drying technology is a viable prospect for the large-scale stabilization of products such as cocoa honey, with less heat exposure compared to other conventional drying methods. This work aimed to evaluate the efficacy of drying adjuvants for a rapid removal of the water present in cocoa honey via atomization, since this process minimizes the effects of glass transition temperature (Tg) related to materials with high sugar contents. Physical parameters such as the moisture content, hygroscopicity, particle size, and yield of the products obtained were determined. Cocoa honey presented 85.3 ± 0.20 g/100 g of moisture. The formulations successfully decreased moisture content, which was lower than 11.72 ± 0.08 g/100 g in the formulations. Water activity ranged between 0.1464 ± 0.0043 and 0.1562 ± 0.029, with no significant difference between the formulations. The hygroscopicity of cocoa honey powders ranged from 29.29 to 29.87 g of water/100 g of cocoa honey. The combination of 20% maltodextrin and 1% whey protein isolate (WPI) led to the best yield, resulting in a free-flowing powder as the final product. On the other hand, the formulation composed of maltodextrin and whey protein isolate in the ratio of 29:1, respectively, led to the most stable product, with less loss of phenolic compounds during the drying process (6.04%). Regarding particle diameter, 90% of the accumulated distribution did not exceed 57 μm. The greatest dispersion of particles occurs in the Ma20W10 formulation with a span of 2.72, inferring greater variation in size between small (7.01 ± 0.06 μm), medium (18.25 ± 0.37 μm), and large (56.65 ± 1.17 μm) particles. The use of whey protein isolate as an adjuvant proved to be an efficient drying process in the production of cocoa honey powder, and was also advantageous for enriching the nutritional content of the final product due to its protein origin. Furthermore, the combination of spray-drying technology and the use of whey protein isolate as adjuvant led to a free-flowing cocoa honey powder with an adequate particle size and benefits in terms of shelf-life extension, providing new opportunities for the commercialization of cocoa honey as an ingredient for the food industry, with benefits for the circular economy.