Uncertainty associated with the result of a measurement can be dominated by the physical sample preparation stage of the measurement process. In view of this, the Optimised Uncertainty (OU) methodology has been further developed to allow the optimisation of the uncertainty from this source, in addition to that from the primary sampling and the subsequent chemical analysis. This new methodology for the optimisation of physical sample preparation uncertainty (u(prep), estimated as s(prep)) is applied for the first time, to a case study of myclobutanil in retail strawberries. An increase in expenditure (+7865%) on the preparatory process was advised in order to reduce the s(prep) by the 69% recommended. This reduction is desirable given the predicted overall saving, under optimised conditions, of 33,000 pounds Sterling per batch. This new methodology has been shown to provide guidance on the appropriate distribution of resources between the three principle stages of a measurement process, including physical sample preparation.