Pulsed electric fields (PEF) are known to influence the chemical and microstructural factors governing apple phenolic compounds fate upon digestion. However, the effect of PEF on fruit phenolic compounds bioaccessibility has yet to be determined. This work assessed the effects of PEF treatment (0 and 24 h after 0.01, 1.8 and 7.3 kJ kg−1) on the bioaccessible and non-bioaccessible fractions of apple phenolic compounds. Bioaccessible and non-bioaccessible 5-caffeoylquinic acid increased at 24 h after delivering 0.01 kJ kg−1 (61 and 35%, respectively). At 1.8 and 7.3 kJ kg−1, the overall bioaccessible content decreased, although the percentage of compounds released (bioaccessibility) increased in some cases. Bioaccessibility of overall phenolic compounds increased from 14% (untreated) to 27% (24 h after 7.3 kJ kg−1). Therefore, PEF processing could modulate the apple functional value, by either increasing phenolic contents in the bioaccessible and non-bioaccessible fractions or the phenolic bioaccessibility.