Tomato flowers (Solanum lycopersicum L.) in greenhouses require assisted pollination. Compared with pollination using a vibration wand, pollination by buzz pollinating bees results in improved seed set and consequently, higher fruit weight. We investigated whether there are further chemical and sensory differences between bee- and wand-pollinated cherry tomatoes, Solanum lycopersicum variety Conchita. The pollination method did not result in significant differences in concentration of soluble solids and titratable acidity. However, the concentration of soluble solids was significantly positively correlated with seed number. We suggest that an increase in the amount of soluble solids in the locular area, due to increased seed numbers, is counteracted by the effects of seed numbers on the growth of the walls, which occurs through cell elongation. In the sensory part of this study, a large, untrained panel significantly preferred bee-pollinated over wand-pollinated tomatoes and classified bee-pollinated tomatoes as having more depth of flavor than wand-pollinated tomatoes. Thus, bee-pollinated tomatoes taste better than wand-pollinated tomatoes, and it is likely that the sensory differences between the two groups of tomatoes are mediated through effects of pollination treatment on seed numbers. Future chemical and sensory studies of fresh tomatoes should take into account the effects of seed numbers and their possible effect on the distribution of chemical compounds within tomatoes.