Onions as an interesting ingredient have been proved to promote Z-isomerization of lycopene and increase bioaccessibility of total-lycopene. Phytoene (PT) and phytofluene (PTF), the precursors of lycopene, are colorless carotenes, which are attracting much attention and are also abundant in tomatoes. Therefore, onions might also affect the distribution and bioaccessibility of PT and PTF isomers during heating tomato (hot-break and cold-break purees)-onion-extra virgin olive oil (EVOO) sauces. The addition of onions (or diallyl disulfide present in onions) into tomato purees did not cause degradation of PT or PTF; however it favored E/Z-isomerization of PT and PTF by reducing the proportions of their natural Z-isomers (Z-15-PT and Z2,3-PTF) and decreased the bioaccessibility of total-PT and total-PTF. Simultaneously, a complex picture was obtained for the effect of onions on the bioaccessibility of individual PT and PTF isomers, depending on the precise isomer. Bioaccessibility of PT and PTF isomers in tomato-based sauces decreased in the order: 15-Z-PT > all-E-PT; Z2,3-PTF > all-E-PTF > Z4 or Z5-PTF total-PT > total-PTF. E-isomerization of PT and PTF enhanced by onions during heating tomato–onion purees decreased their bioaccessibility.