There is considerable interest in the use of naturally derived bioactive compounds (BACs) in the formulation of fortified functional drinks, owing to their health benefits. Yet, industrial scalability raises several challenges, mainly due to their instability in response to external factors such as pH, light, oxygen, temperature, and sugar content. BACs such as vitamins, carotenoids, polyphenols, amino acids, coenzyme Q10, and pre-/probiotics are susceptible to degradation during processing and packaging, which can reduce their effectiveness. In this context, this systematic review aims to study the use of particle engineering as technological means of optimizing these parameters through techniques including nano- and microencapsulation, and high-pressure homogenization. The methodology used is to collect data from relevant databases, such as PubMed and ScienceDirect, and then clean and refine the data using the keywords “particle engineering,” “bioactive compounds,” and “functional beverages.” The year of publication is also limited, and various bibliometric methods are applied. The results show that these methods protect the BACs, boost their solubility, control their release, and preserve their stability in complex liquid matrices. Additionally, factors such as sugar type and quantity, fermentation temperature, and storage time can greatly impact the stability and bioavailability of these compounds. The growing demand for natural products and low-calorie, healthy functional drinks is driving extensive research on optimizing novel ingredients for these trendy beverage categories. In conclusion, this study critically analyzes the technologies used to engineer particles in functional drinks, focusing on how they impact the stability, bioavailability, and effectiveness of BACs, as well as their capacity to optimize the overall quality, food safety, and commercial viability of these items in the food and nutraceutical markets.