Black chokeberry juice production results in a large amount of pomace, which is usually regarded as waste. Nevertheless, it contains significant amounts of anthocyanins, which can be utilized as health-promoting components, but also as food colorants. To take advantage of their benefits, green extraction methods such as microwave-assisted (MAE) and ultrasound-assisted extraction (UAE) are widely used for their isolation. This study aimed to evaluate the effects of MAE and UAE parameters (solvent, treatment time, temperature, or ultrasound amplitude) on the extraction yield of anthocyanins from black chokeberry pomace and to compare the effectiveness of these two green extraction methods with conventional reflux extraction, both in terms of total anthocyanins yield and effects on individual compounds. In both techniques, acidification of the extraction solvent did not show a significant effect on anthocyanin content. For MAE, a temperature increase from 40 to 60 °C positively affected the extraction yield, while 4 min was a substantial treatment time for the extraction. Conversely, UAE required 10 min of treatment time with no effect on amplitude. UPLC ESI-MS2 analysis confirmed the presence of 6 anthocyanins in the obtained extracts, with significantly higher levels of cyanidin-3-O-xyloside and cyanidin-3-O-arabinoside were in ones isolated by green extraction techniques.