A chitosan-glucose derivative (ChG) with lower antimicrobial activity against whey native probiotic yeast K. marxianus VM004 was synthesized by the Maillard reaction. The ChG derivative was characterized by FT-IR, 1H NMR, and SLS to determine the structure, deacetylation degree (DD), and molecular weight (Mw). In addition, we evaluated the antioxidant, cytotoxic, and antimicrobial activities of ChG. ChG was then used for microencapsulation of K. marxianus VM004 by spray drying. The microcapsules were characterized by evaluating their encapsulation yield, encapsulation efficiency, morphology, tolerance to the gastrointestinal tract, and viability during storage. The results indicated that a non-cytotoxic product with lower MW and DD and higher antioxidant activity than native chitosan was obtained by the Maillard reaction. The yeast ChG microcapsules exhibited an encapsulation efficiency >57 %, improved resistance to gastrointestinal conditions, and enhanced stability during storage. These results demonstrate that ChG may be a promising wall material for the microencapsulation of probiotic yeasts. •Chitosan-glucose derivative (ChG) did not show antimicrobial activity against yeast.•ChG is not-cytotoxic and shows higher antioxidant activity than native chitosan.•Mw and deacetylation degree of ChG decreases by approximately 10 %.•Microencapsulation in ChG improved resistance to the gastrointestinal conditions.•Crosslinking microcapsules improves tolerance to the intestinal tract and storage stability.