Probiotics provide significant health benefits, but their viability is often compromised during production, storage, and passage through the gastrointestinal tract. These challenges hinder their effective incorporation into functional applications, particularly in dairy functional foods, in which factors such as acidity, oxygen exposure, and storage conditions negatively impact cell survival. The focus was on functional dairy foods, particularly on pasta filata cheeses. Indeed, the use of probiotics in pasta filata cheeses presents significant challenges due to the specific manufacturing processes, which encompass the application of high temperatures and other harsh conditions. These factors can adversely affect the viability and availability of probiotic microorganisms. However, microencapsulation has emerged as a promising solution, offering a protective barrier that enhances probiotic stability, improves survival rates, and facilitates targeted release in the gastrointestinal environment. This review examines the pivotal role of microencapsulation in stabilising probiotics for functional applications, emphasising its relevance in high-value food systems. Functional applications, including foods designed to offer essential nutritional benefits and promote host health, play a crucial role in disease prevention and immune system support, reducing the risk of infections and other physiological impairments. Key microencapsulation technologies are analysed, focusing on their benefits, limitations, and challenges related to scalability and industrial implementation. Additionally, this review discusses strategies to optimise formulations, ensure the sensory quality of final products, and explore future opportunities for expanding innovative applications that align with growing consumer demand for health-promoting solutions.

Milk represents not only a source of essential nutrients but also a versatile matrix for the development of functional foods when combined with lactic acid bacteria (LAB) fermentation. While cow milk is the most widely consumed, alternative matrices such as goat and donkey milk possess distinctive compositional features that may influence the bioactivity of fermented products. In this work, fifteen different strains belonging to LAB and bifidobacteria were initially tested for their ability to ferment cow, goat, and donkey milk. Fermented samples showing the best acidification rate were further screened for total phenolic content (TPC), radical scavenging activity (RSA), and effects in human colon epithelial cells and Caco-2 adenocarcinoma cells. The results showed that fermentation modulated TPC in a strain- and matrix-dependent manner, with donkey milk showing the most consistent increases. RSA was significantly enhanced in fermented samples, particularly those inoculated with Lacticaseibacillus casei BGP93 and LC4P1 strains and Limosilactobacillus reuteri ATCC23272. Cell viability assays confirmed the absence of cytotoxicity, and fermented milk extracts reduced ROS under induced oxidative stress. Antimicrobial assay showed that Lactiplantibacillus plantarum LPAL selectively inhibited Listeria monocytogenes, with the strongest effect observed in donkey milk. These findings suggest that LAB-fermented milks from goats and donkeys may represent safe functional foods with improved antioxidant and antimicrobial activities.