•PEF-assisted extraction of bio-compounds from apple peels was tested.•The correlations between the electrical conductivity disintegration index, Zc, and cell disintegration, Zd, were determined.•The efficiency bio-compounds (soluble matter content, °Brix, and total polyphenol content, TPC) from apple peels was analyzed.•The correlations between extraction of bio-compounds and Zc were discussed. The pulsed electric field (PEF) assisted extraction of bio-compounds (soluble solids concentration, °Brix, and total polyphenol content, TPC) from apple peels was studied. The aqueous suspensions of apple peels were treated by PEF with different intensities, E (480–1200V/cm), and different treatment times, tPEF (0–2s). The cell disintegration was analyzed using measurement of electrical conductivity (disintegration index, Zc) and microstructure evaluation by confocal laser scanning microscopy (microscopic cell disintegration index, Zd). The near linear Zc (Zd) dependencies were obtained for PEF treatment protocols with different treatment time, tPEF, and electric field intensity, E. The °Brix and TPC extraction efficiencies were dependent upon applied value of E. For example, at the highest PEF intensity, E=1200V/cm, and Zc≈1, the enhancements in values of °Brix and TPC were approximately the same ≈3.15. However, at lower PEF intensities (480, 600 and 800V/cm) and the fixed value of Zc the extraction of soluble matter was more effective compared to TPC. Therefore, the extraction efficiency of different bio-molecules is not only affected by the level of tissue disintegration (by value of Zc). The other details of PEF protocols (e.g., value of E) may be also important.