Medicinal and Aromatic Plant (MAP) by-products constitute a vast reservoir of bioactive metabolites with antioxidant and antimicrobial properties, offering potential for the development of high added value natural products. This study focuses on the by-product (tepals) remaining during the process of receiving the stigma of Crocus sativus L. Iridaceae (saffron), which is the commercially exploitable part of the flowers. The tepals are the main part of the flowers (>95%) and are still discarded in the fields during the collection of the stigmas in Kozani, Greece. According to numerous findings, the saffron tepals are rich in flavonoids with notable biological properties, and our aim was to investigate an alternative for their management. Within this context, dry and frozen tepals were extracted at a laboratory scale through microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE), followed by adsorption resin technology (ART) for the preparation of enriched extracts. Furthermore, their HPTLC profiling, the phenolic (TPC) and flavonoid (TFC) content, and the free-radical-scavenging (DPPH) and anti-tyrosinase activity were evaluated. The frozen tepals were further extracted at a pilot scale using MAE and maceration (Mc) techniques, followed by ART treatment to remove the contained sugars. The enriched extract produced at a pilot scale using MAE and ART sequentially is characterized by a high phenolic (147.2 mg GAE/g dry extract) and flavonoid (114.8 mg QUE/g dry extract) load. These findings demonstrate that saffron tepals, traditionally considered waste, can serve as a valuable raw material for producing extracts rich in phenolic derivatives, particularly flavonoids and anthocyanins.