BACKGROUND Red‐fleshed apples are a great source of natural colorants and functional food ingredients because of their high anthocyanin content. Generally, anthocyanins are highly unstable after extraction, which limits their wide applications in the food and pharmaceutical industries. This study was aimed at investigating the effects of combining copigmentation with encapsulation on the stability of anthocyanins from red‐fleshed apples. In this study, red‐fleshed apple anthocyanins were copigmented with caffeic acid, and then the copigmented complexes were encapsulated using gum arabic and maltodextrin using spray drying and freeze drying. RESULTS All anthocyanin microcapsules had high encapsulation efficiencies ranging from 93.84 to 96.85% with mean hydrodynamic diameter smaller than 350 nm. After heating at 80 °C for 2 h, the dispersions of microencapsulated anthocyanins with copigments exhibited the highest absorbance values at λmax (515 nm) (P < 0.05). Light stability experiments demonstrated that the half‐life of the red‐fleshed apple anthocyanins increased from 5 to 12 days after being treated with copigmentation and encapsulation. The drying methods (spray/freeze drying) did not significantly influence the stability of the microencapsulated anthocyanins. CONCLUSIONS Applying copigmentation and spray‐drying encapsulation in tandem has great potential for enhancing the stability of red‐fleshed apple anthocyanins. Thus, such anthocyanins with enhanced stability may be increasingly used in the food and pharmaceutical industries as value‐added natural food pigments. © 2018 Society of Chemical Industry