Z-lycopene isomers are more bioavailable than all-E-lycopene, especially 5-Z-lycopene. Based on our observations, the addition of unblanched onion could favor Z-isomerization of lycopene (by more than 94%) during heating tomato-onion-extra virgin olive oil (EVOO) purees at 90 °C for 2 h. The increase in Z-lycopene was correlated linearly with the addition of unblanched onion, with R2 > 0.92, and increased rates of 5-Z-lycopene were 3–4 times higher than for 9-Z-lycopene and 13-Z-lycopene. Diallyl disulfide (DADS), formed by alliinasecatalyzed breakdown of non-volatile precursors in onion, contributed to these increases and correlated linearly (R2 > 0.79, 0–0.50 mg/g puree) with increased Z-lycopene. Increased rates of 5-Z-lycopene were also 3–4 times higher than for 9-Z-lycopene and 13-Z-lycopene. However, blanching of onion, in tomato-onion-EVOO purees, before heating, significantly decreased the effect of onion on Z-isomerization of lycopene.