Citrus peel physicochemical attributes are considered the main components conferring partial or even total resistance to fruit fly (Diptera: Tephritidae) infestation. Fruit fly females adapt their ovipositional strategies to overcome such resistance. Here, we explored the effects of citrus species (Rutaceae) on the ovipositional behaviour of the South American fruit fly, Anastrepha fraterculus (Wiedemann), and on its immature development. Particularly, we investigated the effects of (1) citrus species on oviposition behaviour and immature development, (2) citrus species on oviposition preference and on the location of the eggs at different depth in the citrus peel, and (3) harvest season and post‐harvest storage time on oviposition behaviour and immature development in lemon. Citrus species influenced ovipositional behaviour and affected survival of immature stages. Females laid eggs in lemon [Citrus limon (L.) Burm.], orange [Citrus sinensis (L.) Osbeck], and grapefruit (Citrus paradisi Macfadyen). In orange and lemon, larvae were found dead close to the oviposition areas, suggesting chemically mediated resistance mechanisms. Under choice conditions, females preferred grapefruit over lemon and bigger clutches were found in the layers where embryonic development is favoured. Unsuitability of lemon as a medium to complete development was neither affected by harvest season nor by storage time of the fruit after harvest. The physical and chemical characteristics of the peel were distinctive to each citrus species and may have affected the specific levels of resistance of these citrus species to infestation by A. fraterculus.