This study assessed whether chemical analyses are sufficient to guarantee the safety of heat processing of soybeans (SB) for human/animal consumption. The effects of extrusion and dry-toasting were analyzed upon seed composition and performance of broiler chicks. None of these induced appreciable changes in protein content and amino acid composition. Conversely, toasting reduced all antinutritional proteins by over 85%. Despite that, the animals fed on toasted SB demonstrated a low performance (feed efficiency 57.8 g/100 g). Extrusion gave place to higher contents of antinutrients, particularly of trypsin inhibitors (27.53 g/kg flour), but animal performance was significantly (p < 0.05) better (feed efficiency 63.2 g/100 g). Upon the basis of chemical analyses, dry-toasting represents the treatment of choice. However, considering the results of the feeding trials, extrusion appears to be the safest method. In conclusion, in order to evaluate the reliability of any processing method intended to improve nutritional value, the combination of chemical and animal studies is necessary.