Abstract In accordance with Article 6 of Regulation (EC) No 396/2005, the applicant, BASF SE, submitted an application to the competent national authority in Greece to modify the existing maximum residue level (MRL) for the active substance mepiquat in cotton seeds. The data submitted in support of the application were found to be sufficient to derive a MRL proposal for cotton seeds and the previously derived MRL proposals for animal commodities were found to be still valid. Adequate analytical methods for enforcement are available to control the residues of mepiquat chloride in the plant and animal commodities under consideration at the validated limit of quantification (LOQ) of 0.01 mg/kg. Based on the risk assessment results, EFSA concluded that the short‐term and long‐term intake of residues resulting from the use of mepiquat chloride according to the reported agricultural practices is unlikely to present a risk to consumer health.