Background: In insects, oviposition decisions may lead to egg deposition in substrates with different larval density and nutritional levels. Individuals developing in such substrates may present plasticity in their phenotype. Here, we investigated the effect of two factors related to oviposition decisions, namely larval density and substrate quality, on the wing size and wing shape of the stable fly, Stomoxys calcitrans L. (Diptera: Muscidae). Methods: We reared S. calcitrans larvae at different densities (5, 15 and 25) and on different substrates (camel, cow, donkey and sheep dung). For each fly that emerged, we recorded body weight, and detached, slide-mounted and photographed the right wing. Next, we collected 15 landmarks on each photographed wing, and applied geometric morphometric analysis to assess variation in wing size and wing shape of S. calcitrans across the different larval densities and substrate types. Results: We observed that wing size and wing shape of S. calcitrans were affected by larval density and the nature of the developmental substrate. Flies reared in a group of 5 had larger wing centroid size, wing length, wing width, wing area and wing loading compared with those reared in a group of 25. Also, flies developed in donkey and sheep dung had larger wing centroid size, wing length, wing width, wing area and wing loading in comparison with those grown in camel and cow dung. Canonical variate analysis followed by discriminant analysis revealed significant wing shape variation in S. calcitrans across the different densities and substrates. Wing size had a significant but weak positive effect on wing shape. Conclusions: This study demonstrates the high sensitivity of S. calcitrans wings to variation in larval density and developmental substrate, and that use of landmark-based geometric morphometric analysis could improve our understanding of how flies of veterinary importance respond to environmental variability.