Ultrasound-assisted aqueous extraction (UAE) of soluble matter (°Brix), catechin and total phenolic contents (TPC) from flesh and peel of apple tissues were studied. The commercial green (Granny Smith) and red (Red delicious) apples were used in the investigation. All extractions were done at fixed temperature, T = 50 °C, and protocols with different specific energy inputs, S1 (W = 0 kJ/kg), S2(W ˜ 6.5 kJ/kg), S3(W ˜ 10.6 kJ/kg), S4(W ˜ 21.3 kJ/kg), and S5(W ˜ 26.8 kJ/kg) during the initial period of extraction (first 300–350 s). The total aqueous extraction time was up to 3 h. The kinetics of extractions, and correlations oBrix and concentration of catechin, C were compared for flesh and peel tissues. The increase of energy resulted in increase of oBrix and C values. For both green and red apples, the values of°Brix and C were noticeably higher for peel as compared to flesh. The distinct correlations between saturation levels of Cm and TPCm at the long extraction time (≈3 h) were observed. However, the relative content of catechin in TPC (i.e., ratio Cm/TPCm) evidenced the presence of selectivity in extraction of catechin. This selectivity depends from the type of tissue (flesh or skin), apple variety (green or red) and applied treatment protocols.