Knowledge about indirect defences that mediate the ecological interactions between plants and their beneficial and harmful insects are needed to better incorporate pest resistance traits in breeding programs. “Top-down” pest control by natural enemies has not been considered in most plant breeding strategies and, in many cases, beneficial interactions of crops with the third trophic level have been reduced through breeding processes. Extrafloral nectaries (EFNs) are plant structures that provide indirect defences to plants through nectar rewards attracting arthropods that may act as predators of pests. Recent studies have demonstrated that EFNs may play an important role in herbivore suppression in agricultural systems. The main objectives of this study were to quantify the leaf extrafloral nectar production of cotton plants, to identify natural enemies of crop pests visiting these EFNs, and to assess the biological control and occurrence of various cotton pests. To address these objectives, we performed both greenhouse and field experiments in which we compared three wild varieties of cotton plants with EFNs, two cultivated varieties with EFNs and two nectariless varieties. Results showed that wild cotton varieties produced greater quantity of nectar per leaf than cultivated varieties. In addition, wild varieties bearing EFNs enhanced the diversity of natural enemies (especially ants) which could, in turn, increase biological control under certain conditions. However, the association between the community of insects visiting EFNs and pest suppression was not clear and depended on the pest species. Indirect defences associated to EFN need to be better explored to enhance selection of pest-resistant cotton cultivars.