Microneedles (MN) are short, sharp structures that have the ability to painlessly pierce the stratum corneum, the outermost layer of the skin, and interface with the dermal interstitial fluid that lies beneath. Because the interstitial fluid is rich in biomarkers, microneedle-based biosensors have the potential to be used in a wide range of diagnostic applications. To act as an electrochemical sensor, the tip or the body of the MN must be functionalized, while the substrate areas are generally passivated to block any unwanted background interference that may occur outside of the skin. This work presents four different passivation techniques, based on the application of SiO2, polymethyl methacrylate (PMMA), an adhesive film, and varnish to the substrate areas. Optical, SEM and electrochemical measurements were performed to quantitatively assess the performance of each film. The data shows that whilst manual application of varnish provided the highest level of electrical isolation, the spin-coating of a 5 μm thick layer of PMMA is likely to provide the best combination of performance and manufacturability. Clinical Relevance- Substrate passivation techniques will improve the performance of microneedle-based non-invasive continuous monitoring systems.