Tomatoes, the major sources of lycopene in human diet, are often processed into multi-ingredient products that contain vegetable oil and onion. Microwave heating (250W for 20 min) tomato-based purees in the presence of both onion and extra virgin olive oil (EVOO) clearly promoted Z-isomerization of lycopene and increased transfer of lycopene into oil (expressed as partition factor (PF) between tomato-based puree and oil), while only PF increased with either one of both ingredients. The proportion of Z-lycopene and PF increased with the addition of onion (10–50%) and EVOO (1–10%). This increase could be fitted with a linear equation, with R2 over 0.807. Microwave heating time (0–30 min at 250 W) also promoted Z-isomerization of lycopene and PF (R2 over 0.910), and among different microwave heating combinations (power, time), the combinations of high power and short time had greater effects. The PF of total-Z-lycopene was higher than that of all-E-lycopene. The proportion of total-Z-lycopene and 5-Z-lycopene present in the tomato-based purees after the same microwave treatment was positively correlated with the PF of total lycopene, with R2 higher than 0.690 (p=0.0008), which illustrated that the increased proportion of Z-lycopene with onion and EVOO could contribute to enhanced transfer of lycopene.