Tomato improvement is essential for enhancing processing quality and maximizing antioxidant retention in value-added products. This study aimed to evaluate compositional changes and nutrient retention in fresh and thermally processed fruits of diverse tomato genotypes, including double-cross hybrids derived from four single-cross parents and hybrids developed between purple and cherry tomato lines. Fresh tomatoes and thermally processed tomato puree samples were analysed for lycopene, β-carotene, ascorbic acid, anthocyanin, titratable acidity and total soluble solids (TSS). Highly significant genotypic variation was detected for all quality traits, indicating strong genetic control. PAN12023, a single-cross hybrid genotype, exhibited the highest TSS and lycopene content. Thermal processing led to substantial increases in lycopene levels (673.89 %), especially in purple × cherry and double-cross hybrids, while other nutrients generally declined. Among the hybrids, Bidhan Purple × Cherry Yellow Big Fruit showed the greatest retention of β-carotene, ascorbic acid, anthocyanin and titratable acidity despite processing losses. Standardizing appropriate thermal processing techniques and utilizing multi-parent hybridization can provide genetically diverse germplasm and support the breeding of improved tomato varieties with enhanced nutritional resilience. Overall, the results highlight the importance of genotype selection for developing nutrient-rich processed tomato products having a wide range of health benefits as well as maintaining the consumer preferences.