A methodology based on a solid phase extraction (SPE) was optimized for the recovery of phenolic compounds from the spent fermentation broth generated from Biofene® (trans-β-farnesene) production. For this purpose, two resins (XAD-2 and HP-20) and three desorption solutions (water, 50/50 ethanol/water, and ethanol) were tested. The most efficient resin revealed to be the HP-20, using ethanol as desorption solution, reaching an overall total phenolic compound recovery of ca. 80% when 6 BV (bed volume) of both feed and ethanol were applied. The optimization of the resin’s process cycle pointed to 15 BV feed to be treated per cycle and using the same volume of ethanol in the desorption step, with no need for an extra resin regeneration step, stably yielding 48% total phenolic compound recovery from the spent broth for at least 4 cycles, translating into 60 BV of feed being treated per BV of resin, and with the resin being still perfectly active. The extract was characterized using LC−ESI−UHR−QqTOF−MS, and a total of 82 and 15 compounds were identified, in negative and positive ionization modes, respectively. Organic acids were the main class of compounds identified in the phenolic-rich extract, followed by phenolic compounds, saccharides, peptides or amino acids and vitamins. Additionally, the extract revealed a significant antioxidant capacity (914.1 ± 51.6 and 2764.5 ± 142.8 µmol Trolox equivalents/g-dw, respectively, with ABTS and ORAC methodologies), which might be interesting for a wide variety of applications.