Environmental exposure to pesticide mixtures is an increasing public health concern, yet their combined effects on DNA conformational integrity and protein structural stability remain insufficiently characterized under controlled in vitro conditions. This study examined the individual and combined effects of two widely used pesticides, imidacloprid and cymoxanil, on plasmid DNA conformational integrity and BSA structural stability. Using plasmid relaxation and SDS-PAGE assays, pBluescript M13+ plasmid DNA and bovine serum albumin (BSA) were exposed to increasing concentrations (50–800 μg/mL) of each pesticide. Both compounds induced detectable plasmid DNA conformational alterations, with co-exposure leading to the complete loss of the supercoiled DNA form, suggesting more pronounced DNA structural alteration under combined exposure. While imidacloprid alone had limited effects on the BSA band pattern, cymoxanil induced mild BSA structural alterations; their combination resulted in more evident changes in BSA band intensity and structural integrity. These findings suggest that pesticide co-exposure may intensify molecular structural alterations under the present in vitro conditions and support the need for mixture-based toxicological assessment.