We investigated the effect of cultivation system (conventional or organic), cooking method, and flesh color on the contents of ascorbic acid (AA) and total phenolics (TPs), and on total antioxidant activity (Trolox equivalents, TE) in Solanum tuberosum (potato) tubers. The research material, consisting of 4 potato cultivars, was grown in experimental fields, using organic and conventional systems, at the experimental station in 2012 and 2013. The analysis showed that organically grown potatoes with creamy, light yellow, and yellow flesh had significantly higher TPs than did potatoes grown conventionally. Flesh color and cooking method also affected AA. The greatest losses of AA occurred in yellow-fleshed potatoes grown conventionally and cooked in the microwave; such losses were not observed in potatoes grown organically. A dry cooking method (baking in a microwave) increased the TP contents in potatoes by about 30%, regardless of the flesh color and the production system. TE was significantly higher in organically grown potatoes (raw and cooked in a steamer) than in conventionally grown potatoes. TE and AA contents showed a significant positive correlation, but only in potatoes from the organic system [R2 = 0.686]. By contrast, the positive correlation between TE and TPs was observed regardless of the production system. Therefore, we have identified the effects of farming system, cooking method, and flesh color on the contents of bioactive compounds in potato tubers.