Multi-mycotoxin determination by LC-MS is commonly based on external solvent-based or matrix-matched calibration and, if necessary, the correction for the method bias. In everyday practice, the method bias (expressed as apparent recovery RA), which may be caused by losses during the recovery process and/or signal/suppression enhancement, is evaluated by replicate analysis of a single spiked lot of a matrix. However, RA may vary for different lots of the same matrix, i.e., lot-to-lot variation, which can result in a higher relative expanded measurement uncertainty (Ur). We applied a straightforward procedure for the calculation of Ur from the within-laboratory reproducibility, which is also called intermediate precision, and the uncertainty of RA (ur,RA). To estimate the contribution of the lot-to-lot variation to Ur, the measurement results of one replicate of seven different lots of figs and maize and seven replicates of a single lot of these matrices, respectively, were used to calculate Ur. The lot-to-lot variation was contributing to ur,RA and thus to Ur for the majority of the 66 evaluated analytes in both figs and maize. The major contributions of the lot-to-lot variation to ur,RA were differences in analyte recovery in figs and relative matrix effects in maize. Ur was estimated from long-term participation in proficiency test schemes with 58%. Provided proper validation, a fit-for-purpose Ur of 50% was proposed for measurement results obtained by an LC-MS-based multi-mycotoxin assay, independent of the concentration of the analytes.Electronic supplementary materialThe online version of this article (10.1007/s00216-018-1096-5) contains supplementary material, which is available to authorized users.