Avocado peels are the main agro-industrial residue generated during the avocado processing, being a rich source of bioactive compounds like phenolic compounds. The growing demand for more sustainable processes requires the development of new and effective methods for extracting bioactive compounds from industrial waste. Deep eutectic solvents (DESs) are a new sustainable alternative to toxic organic solvents due to their non-toxicity and biocompatibility. In this study, five selected DESs were applied for the extraction of bioactive phenolic compounds from avocado peels. The extraction efficiency was evaluated by measuring the total phenolics and flavonoids content. The best extraction results were obtained with choline chloride-acetic acid and -lactic acid (92.03 ± 2.11 mg GAE/g DAP in TPC and 186.01 ± 3.27 mg RE/g DAP); however, all tested DESs show better extraction efficiency than ethanol. All the obtained NADES extracts have high antioxidant activity (FRAP: 72.5–121.1 mg TE/g; TAC: 90.0–126.1 mg AAE/g). The synthesized DESs and avocado peels DES extracts had activity against all tested bacteria (Staphylococcus aureus, Streptococcus dysgalactiae, Escherichia coli and Pseudomonas putida), and the extracts prepared with choline chloride-acetic acid and -lactic acid have the highest antibacterial activity against all microorganisms. These results, coupled with the non-toxic, biodegradable, low-cost, and environmentally friendly characteristics of DESs, provide strong evidence that DESs represent an effective alternative to organic solvents for the recovery of phenolic bioactive compounds from agro-industrial wastes.