In accordance with Article 6 of Regulation (EC) No 396/2005, the evaluating Member State (EMS), United Kingdom, received an application from Bayer CropScience S.A.S. to modify the existing maximum residue level (MRL) for the active substance prothioconazole in shallots. In order to accommodate for the intended use of prothioconazole, United Kingdom proposed to set the MRL at the limit of quantification (LOQ) of 0.05 mg/kg. According to EFSA the data are sufficient to derive a MRL proposal of 0.05 mg/kg (LOQ) for the intended use on shallots in northern Europe. Adequate analytical enforcement methods are available to control the residues of prothioconazole-desthio in the commodity under consideration. Based on the risk assessment results, EFSA concludes that the proposed use of prothioconazole on shallots will not result in a consumer exposure exceeding the toxicological reference values and therefore is unlikely to pose a consumer health risk. However, the consumer risk assessment should be regarded as provisional since the possible contribution of the triazole derivative metabolites (TDMs) in the consumer risk assessment was not taken into consideration.