In the sustainability framework, valorization of organic by-products as reservoirs of phytochemicals useful for human health represents a hot topic. Therefore, this study evaluated Norway spruce bark and twigs (NSB, NST), chestnut tree wood (CTW), and pomegranate fruit waste/pomace (PFW) as sources of bioactive compounds by employing green technologies. Microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE), applied individually or sequentially, were optimized by modulating solvent composition, temperature, time, microwave power, and ultrasound amplitude. Hydroalcoholic extraction (50% ethanol) combined with MAE yielded the highest phenolic recovery and antioxidant activity across all matrices. PFW exhibited the highest antioxidant activity assessed through FRAP, ORAC, and DPPH assays. Phytochemical profiling by HPLC-DAD identified stilbenes in spruce extracts, ellagic acid in chestnut wood, and ellagic acid and punicalagins in pomegranate waste as major bioactive constituents. Additionally, NSB and PFW exhibited α-amylase inhibitory activity. Antimicrobial testing demonstrated dose-dependent activity against Gram-positive (Staphylococcus epidermidis and Bacillus subtilis) and Gram-negative (Pseudomonas stutzeri) strains, with PFW exhibiting the strongest inhibition and NSB displaying broad-spectrum effects. Total phenolic content changed moderately after 21 days of storage. These results demonstrate that sustainable extraction enables efficient recovery of bioactive compounds from plant by-products, supporting their further functional, dietary, and medicinal applications.