A reassessment of factors related to milk production economics is needed because of continuing genetic improvements within the main dairy breeds and changes in farm management and the economic environment. Therefore, in this study, we aimed to evaluate the development of economic indicators between 2016 and 2020 on Czech dairy farms that kept either Czech Fleckvieh or Holstein breeds and that had different average milk yields. We used a questionnaire to obtain data from 66 dairy farms from different regions of the Czech Republic. The farms were divided into four groups according to breed and 2016 milk yield. Production costs increased during the period in all groups by 13% to 17% because of increasing milk yields, the associated higher feed consumption and increasing input prices. We observed a higher annual growth rate of costs per litre of milk on farms with above-average milk yields compared with the groups with below-average yields. The highest profitability before subsidies was achieved on farms with Holstein cows and above-average milk yields. Higher-income over feed costs were consistently observed in groups with higher milk yields. Because of low farm gate milk prices, profitability was significantly lower across all groups during 2016 than in other years.