In compliance with Article 43 of Regulation (EC) No 396/2005, EFSA received from the European Commission in 2020 a mandate to provide its reasoned opinion on the toxicological properties and maximum residue levels (MRLs) for the benzimidazole substances carbendazim and thiophanate‐methyl. Specifically, EFSA was asked to assess whether thiophanate‐methyl or carbendazim has clastogenic potential and, in case clastogenic potential can be excluded, to derive toxicological reference values necessary for consumer risk assessment and assessment of maximum residue levels (MRLs). Although these active substances are no longer authorised within the European Union, MRLs were established by the Codex Alimentarius Commission (codex maximum residue limits; CXLs), and import tolerances are in place. Based on the assessment of the available data, toxicological reference values and MRL proposals were derived and a consumer risk assessment was carried out. Some information required by the regulatory framework was found to be missing and a possible acute risk to consumers was identified. Hence, the consumer risk assessment was considered indicative only and all MRL proposals derived by EFSA still require further consideration by risk managers. In October 2022, to ensure that MRLs derived by EFSA in its assessment of 2021 are safe for consumers also in view of endocrine‐disrupting properties, EFSA was requested to carry out a follow‐up assessment taking into account the scientific criteria for identifying endocrine disruptors (ED). Based on the outcome of the assessment, the experts agreed that the reference values are also covering the concern related to the identified hazards indicative of endocrine disruption for thiophanate‐methyl. No further considerations on the impact of the ED assessment on the current reference values were needed for carbendazim since the ED criteria are not met for this substance. Therefore, the risk assessment and the MRL recommendations derived in 2021 are confirmed.