Strawberry (Fragaria × ananassa, Duch.) represents a relevant source of micronutrients and phenolic substances, most of which are natural antioxidants and contribute to the high nutritional quality (NQ) of the fruit. Despite its proven health benefits, strawberries also contain allergenic compounds. In particular protein Fra a 1 is considered the main cause of allergic reactions after consumption of these fruits. However, there is a dearth of literature data on the genetic and seasonal influences on the Fra a 1 accumulation in strawberries, and on the quantitative variation of this allergen during fruit ripening.The aim of the present study was to evaluate and compare the total antioxidant capacity and vitamin C, phenolic, protein and allergen contents of four strawberry genotypes. Two commercial varieties, “Adria” and “Sveva”, and two advanced selections originating from the Marche Polytechnic University strawberry breeding program, “AN94.414.52” and “AN00.239.55”, were selected for this study. To assess the genotype and seasonal influence on the strawberry nutritional and non-nutritional traits, strawberries in three different ripening stages were analysed during the fruiting seasons 2007 and 2008. In the 2-year evaluation, the ripe red fruits of the cultivar “Sveva” showed the highest TAC, phenolic and flavonoid contents and interestingly the lowest allergen content. However, the variety “Sveva”, together with the F2 selection “AN00.239.55”, were the most affected by the year-to-year variability of temperature observed in the nutritional and non-nutritional aspects of the fruits. These findings confirmed a relevant genotype-dependent response to environmental stress conditions, which may in part explain the changes in the antioxidant, phenolic and allergenic properties of strawberry fruits in different years.