A lifelong feeding study with soybean from different production systems was carried out in the crustacean Daphnia magna (water flea), an acknowledged model organism for ecotoxicological studies. Experimental diets were prepared with soybean meal from different agriculture production systems: (i) genetically modified Roundup-Ready soy (Glyphosate-Tolerant), (ii) conventional soy and (iii) soy from organic agriculture (agriculture with neither synthetic pesticides nor synthetic fertilizers). Overall, feed produced from organic soybeans resulted in the highest fitness (higher survival, better growth and fecundity) in the model organism. Animals fed Roundup-Ready soybean consistently performed less well compared to animals fed either conventional or organic soybeans. We conclude that accumulation of herbicide residues in Roundup-Ready soy and related nutritional differences between the soy types may have caused the observed fitness differences. The results accentuate the need for further research clarifying qualitative aspects, including potential large-scale consequences for food and feed quality, of this dominant crop.