Sour cherry (Prunus cerasus L.) is rich in polyphenols which are known to be protective agents against several diseases. Polyphenols are highly sensitive against temperature, pH, oxygen, and light conditions, leading to low bioaccessibility. In this study, polyphenols of sour cherry concentrate (SCC) were encapsulated by uniaxial or coaxial electrospinning with gelatin or gelatin-lactalbumin. Results showed that phenolic acids had higher encapsulation efficiencies than anthocyanins. Encapsulation efficiencies were found as 89.7 and 91.3% in terms of phenolic acids and 70.3 and 77.8% in terms of flavonoids for the uniaxially electrospun samples with gelatin and gelatin-lactalbumin, respectively. The content of polyphenols in SCC decreased after intestinal tract whereas all electrospun samples showed improved bioaccessibility. According to in vitro digestion results, electrospinning encapsulation provided 8 times better protection of cyanidin-3-glucoside compared to the non-encapsulated SCC. Results showed that especially coaxial electrospinning encapsulation is an effective method for sour cherry polyphenols.