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Protease inhibitors (PIs) interfere with digestion, leading to poor nutrient absorption and decreasing amino acid availability in insects. Ingestion of PIs can delay development, cause anatomical malformations, reduce fertility and change the set of proteases in the insect gut. This study evaluated the proteomic profile in the midgut of Anticarsia gemmatalis fed on synthetic (Berenil® with a bis‐benzamidine as active ingredient) and natural (SKTI) protease inhibitors and their effect on the gut physiology, proteolytic activity and the structural characteristics of the trypsin‐inhibitor binding. Larger numbers of protein isoforms were identified specially related to protease activity and stress processes, being that the synthetic PI triggered a lower reprogramming than SKTI. Furthermore, Berenil also promoted higher reduction on midgut protease activity at first times of PI treatment. Molecular modelling of the interactions between the identified proteases and PIs indicated that Berenil can interact with the trypsin enzymes and access to a more hydrophobic site promoting the inhibitory effect on serine proteases. Besides, its inhibitory capacity and structural damage on the midgut cells was sped up possibly by the delay in the expression of proteases, the reprogramming less extensive and the lower expression of upregulated isoforms. Thus, the integration of our results shows that the use of synthetic PIs, such as Berenil, can be efficient for the management of A. gemmatalis.