This research aimed to develop a mango juice microcapsule with high fructooligosaccharides (FOS) content using enzymatic hydrolysis with Novozym® 960 and Pectinex® Ultra SP-L. Enzymatic hydrolysis was done by varying factors which included enzyme concentration (0.1 and 0.2 mL Novozym® 960/100 mL sample and 0.5 and 1.0 mL Pectinex® Ultra SP-L/100 mL sample), incubation temperature (45–55 °C) and incubation time (60 and 120 min). Using 0.2 mL/100 mL sample of Novozym® 960 reduced sugar content by converting 80% of sucrose and increasing FOS levels by 20%. The optimal condition for spray drying increased-FOS mango juice microcapsules were established with 160 °C inlet temperature. Encapsulating agents were; resistant maltodextrin (RM), gum arabic (GA), and a combination of both at 1:1, 2:1, and 3:1 v/v ratios. Microcapsule powders exhibited a light greenish-yellow hue and optimal conditions involved a 3:1 ratio of RM and GA (GRM), which exhibited the highest phenolic compounds, flavonoid content, and antioxidant activity (p ≤ 0.05). Microcapsules stored in vacuum-sealed aluminum bags best maintained physicochemical and microbial quality over a 45-day period. Microencapsulated mango juice has potential to be used in the food industry, including its role in beverage production and as a component in functional foods. •Fructooligosaccharide (FOS) was produced in mango juice by using enzymatic hydrolysis.•The highest FOS production in mango juice was 20% using Novozym® 960.•Microcapsule from a 3:1 ratio of G + RMD exhibited the highest antioxidant property.•Vacuum-sealed aluminum bag was best condition to preserve microcapsule's quality during storage.