The demand for organic food products is steadily increasing partly due to the expected health benefits of organic food consumption. Polyphenols, such as flavonoids and phenolic acids, are a group of secondary plant metabolites with presumably beneficial health effects, and contents in plants are affected by, for example, plant nutrient availability, climate, pathogen infection, and pest attack. In the current study, onions, carrots, and potatoes were cultivated in two-year field trials in three different geographical locations, comprising one conventional and two organic agricultural systems. The contents of flavonoids and phenolic acids in plants were analyzed by pressurized liquid extraction and high-performance liquid chromatography-ultraviolet quantification. In onions and carrots, no statistically significant differences between growth systems were found for any of the analyzed polyphenols. On the basis of the present study carried out under well-controlled conditions, it cannot be concluded that organically grown onions, carrots, and potatoes generally have higher contents of health-promoting secondary metabolites in comparison with the conventionally cultivated ones.