Identifying multitarget impurities on contact lenses is challenging because traditional methods such as polymerase chain reaction cannot be used on the unknown target. Other sampling methods often require expensive antibodies or dyes. Therefore, this research focuses on the detection of multitarget impurities in situ on the lens surface as a more innovative and effective label-free assay using scanning electrochemical microscopy (SECM). Impurities were investigated using an electrochemical assay and an oxygen consumption assay. The electrochemical activity of BSA and the bacteria adhered to the contact lenses was explored using a FcMeOH solution. The experimental results revealed the difference in current values of the clean and protein-adsorbed contact lens samples. Furthermore, SECM can be used to detect the oxygen consumption of aerobic microbes using the oxygen reduction method. Thus, contaminated microbes can be identified without labeling in phosphate buffer saline. The mass spectra of the contact lenses were studied and the adsorption of impurities was verified. Finally, contact lens samples were investigated from various patients with ocular infection diagnosed with corneal ulcers, preseptal cellulitis, and orbital cellulitis. As a result, SECM could be a new tool for distinguishing the cleanliness of contact lenses in the future.