p-Coumaroyl-6́-secologanoside (comselogoside) is a secoiridoid identified in large amounts in olive fruits, although no studies in vitro or in vivo of comselogoside have been reported. This work focuses on the recovery and purification of this compound from olive mill waste (alperujo). The successive isolation on Amberlite XAD-16 and Sephadex LH-20 resins, allowed a comselogoside extract with 80–85% of purity. A photoisomerization of the vinyl-double bond in the p-coumaroyl moiety occurred when the extract was exposed to ultraviolet radiation and a mixture of the trans and cis-isomers was obtained. Both isomers were characterized using NMR, mass spectroscopy, and UV spectrometry. The J (coupling constant) of the protons on the C7 and C8 on the unsaturated chain were found to be the difference between cis (12.8 Hz) and trans- (15.9 Hz) comselogoside. Cis-isomer exhibited lower radical-scavenging activity than trans, although a synergistic effect occurred when the cis-isomer was supplement by the trans-isomer.