Biomass resulting from food production represents valuable material to recover different biomolecules. In our study, we used apple pomace to obtain pectin, which is traditionally extracted using mineral acids. Our hypothesis consisted of carrying out extractions with organic acids, assisted by ultrasound, by varying processing parameters including time, temperature, and type of acid. The analytical determinations of galacturonic acid content, methoxylation and esterification degree, ζ-potential and extraction yield were used as pectin quality indicators. Pectins extracted using treatment conditions with better performance were assessed biologically in vitro for their potential to be used in biomedical applications. Overall, the extracted pectin presented a galacturonic acid content, methoxylation and esterification degree ranged from 19.7 to 67%, 26.8–41.4% and 58–65.2% respectively, and were negatively charged (− 24.1 to − 13.2 mV). It was found that factors of time and temperature greatly influenced the response variables excepting the esterification degree, while the acid type influenced the ζ-potential, methoxylation and esterification degrees. Additionally, it was seen that the longer extraction time (50 min) and higher temperature (50 ◦C) exhibited the better extraction yield (~10.9%). Finally, the selected pectin showed high cytocompatibility up to 500 μg/mL of concentration when seeded with Neonatal Normal Human Dermal Fibroblasts.