Although genetically engineered crops producing insecticidal Cry proteins from Bacillus thuringiensis (Bt) are grown worldwide, few studies cover effects of Bt crops or Cry proteins on dipteran species in an agricultural context. We tested the toxicity of six purified Cry proteins and of Bt cotton and Bt maize tissue on Drosophila melanogaster (Diptera: Drosophilidae) as a surrogate for decomposing Diptera. ELISA confirmed the presence of Cry proteins in plant material, artificial diet, and fly larvae, and concentrations were estimated. Median concentrations in emerging adult flies were below the limit of detection. Bioactivity of purified Cry proteins in the diet was confirmed by sensitive species assays using Heliothis virescens (Lepidoptera: Noctuidae). Purified Cry1Ab, Cry1Ac, Cry1B, Cry1C, Cry1F, or Cry2Aa, or leaf material from stacked Bt cotton (Bollgard II producing Cry1Ac and Cry2Ab) or Bt maize (SmartStax producing Cry1A.105, Cry1Fa2, Cry2Ab2, Cry3Bb1, Cry34Ab1 and Cry35Ab1) had no consistent effects on D. melanogaster survival, developmental time, adult body mass or morphometrics. However, D. melanogaster showed longer developmental time and smaller wing size when fed with cotton leaves from plants infested with H. virescens caterpillars compared to flies fed with leaves from uninfested plants, while no such effects were obvious for maize.