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Granaticins are natural pigments derived from microorganisms with promising bioactivity. However, their practical applications have been restricted due to inherent instability. To improve the stability of granaticins from the novel strain Streptomyces vilmorinianum YP1, microcapsules were prepared using gum Arabic (GA) by a freeze-drying method. The optimal parameters for microencapsulation were determined using response surface methodology. Under the optimal conditions (GA 9.2% (v/v), a wall/−core ratio 4.8 (w/w), encapsulating temperature 29 °C), the maximum encapsulation efficiency achieved was 93.64%. The microcapsules were irregular single crystals with an average particle size of 206.37 ± 2.51 nm. Stability testing indicated improved stability of the microencapsulated granaticins. Notably, granaticnic B retention increased by 17.0% and 6.6% after exposure to sunlight and storage at 4 °C, respectively. These finding suggest that GA as a well material significantly enhances the stability of granaticins from S. vilmorinianum YP1, facilitating their potential applications.