Loading active ingredients on nanocarrier systems is becoming a common strategy for improving pesticide formulations. One of the most important properties of these nanoformulations is the proportion of pesticide associated with the nanocarriers (encapsulation efficiency, EE). EE is often determined by centrifugal ultrafiltration. However, the losses of active ingredient in the centrifugal ultrafiltration devices are typically not assessed, potentially leading to erroneous results. In this work, the losses of three pesticides (tebuconazole, terbuthylazine and chlorpyrifos) during centrifugal ultrafiltration have been systematically evaluated for nine different devices. Results suggest that centrifugal ultrafiltration is not suitable for determining the EE of compounds such as chlorpyrifos as 100% losses were observed on all the devices tested. Losses of tebuconazole and terbuthylazine were highly variable according to the type of membrane and the lowest losses were observed in the devices with hydrophilic regenerated cellulose membranes. Based on these results, we propose a correction factor and demonstrate its application to calculate the EE of two nanoformulations based on poly(ε-caprolactone) nanocarriers. The approach extends the applicability of centrifugal ultrafiltration to a wider range of pesticide nanoformulations. We also discuss the effect of dilution on EE and make recommendations to improve the characterisation of nanoparticles-based pesticide nanoformulations in the future.