The natural wine movement has gained significant attention due to its emphasis on minimal intervention and sustainability. This study investigates the pesticide residues and mycotoxins in natural and conventional wines from Italy and Spain. A total of 46 wine samples were analyzed, divided between countries and production methods. Twenty pesticides were detected, all within the maximum residue limits (MRLs) established for grapes intended for wine production in the European Union. In general, conventional wines showed significantly more residues than natural wines across both regions. Italian wines exhibited higher pesticide residue levels compared to Spanish wines, with some pesticides such as dimethomorph and metalaxyl more frequently detected and at higher concentrations, even in natural production wines. Only fumonisin B2, a mycotoxin typically associated with cereals, was detected in just one conventional Italian sample. Overall, the results underscore the benefits of natural wine production in reducing pesticide residues, though proper implementation of these practices is crucial, as evidenced by the pesticide presence in natural wine samples.