The excess presence of calcium carbonate (CaCO3) in soil poses challenges for production of horticultural crops, including tomatoes. This condition is prevalent in arid and semi-arid regions of Afghanistan. The objective of this study was to evaluate the effects of elevated concentrations of CaCO3 on growth, physiology, and quality attributes of tomato. Seedlings were exposed to different concentrations of CaCO3 (0%, 2.5%, 5%, 10%, and 20% w/w) in soil. The results showed that elevated concentrations of CaCO3 (10% and 20%) significantly increased soil electrical conductivity (EC) and pH, and subsequently affected growth, physiology, and quality of tomato. CaCO3 effects resulted in an increase in leaf electrolyte leakage, leaf calcium content, root respiration rate, root ethylene production, fruit firmness, total soluble solids, ascorbic acid, and organic acids, as well as a decrease in plant height, leaf length, leaf magnesium content, leaf SPAD value, number of leaves per plant, root weight and length, and root activity. At higher concentrations, CaCO3 decreased number of flowers and fruit per plant, as well as fruit weight and diameter, consequently affecting yield production. Although elevated concentrations of CaCO3 is characteristic of soils in Afghanistan, limited information is available about this topic. These findings enhance our understanding of soil conditions in the country and provide valuable insights for farmers.