This study analyzed the residue depletion kinetics of ivermectin (IVM) in Nelore and crossbred (Nelore x Angus) cattle aiming to compare the profiles between the breeds and evaluate the residue levels at the injection site. IVM 1%, at a dose of 0.2 mg/kg, was administered via the subcutaneous route, and tissue samples were collected on different days post administration for analysis by LC–MS/MS. The results revealed that the detection of the marker residue in conventional matrices such as the liver, perirenal fat, and trapezius muscle (injection site) had relatively high residue concentrations. The maximum residue limit (MRL) was exceeded at the injection site at 21- and 35-days post administration in crossbred and Nelore animals, respectively, with significant variations between animals. This study highlighted significant challenges in accurately determining the pharmacokinetic profile and withdrawal periods of IVM in cattle due to high variability in tissue residue data, particularly at injection sites. The comparison of IVM concentrations between cattle breeds was hindered by high standard errors, emphasizing the need for more rigorous sampling protocols. The results suggest that current guidelines may not adequately account for the erratic depletion kinetics of injectable formulations like IVM, especially at injection sites. Therefore, improving sampling techniques and revising guidelines are essential for accurate residue monitoring and withdrawal period determination.