Abstract Potato tubers, which are one of the richest sources of antioxidants, are always cooked before human consumption. The objective of this study was to understand the effects of various domestic cooking methods, i.e., boiling, microwaving and baking on total phenolics, flavonoids, flavonols, lutein, anthocyanins and antioxidant activities in 5 cultivars and 9 advanced selections with different skin and flesh colors after 6 months of storage. The three cooking methods reduced the levels of these compounds and the percentage of DPPH (2,2-Diphenyl-1-pikryl-hydrazyl) radical scavenging activity in all the cultivars and selections. Boiling minimized these losses. Red fleshed tubers contained more flavonoids, whereas purple tubers contained more flavonols. Despite severe loss of these compounds due to cooking, both the flesh types retained larger amounts of all these compounds due to higher initial levels. Decline in the radical scavenging activity is directly related to loss of these compounds due to cooking treatments in all white and colored flesh tubers. Red and purple fleshed tubers exhibited greater radical scavenging activity than yellow and white fleshed tubers after each of the cooking treatments. Correction procedures were introduced to exclude interfering compounds (ascorbic acid, other oxidizing agents and reducing sugars) in Folin-Ciocalteu Reagent (FCR) assay of estimating total phenolics in potato.