Combining specific recognition capabilities with the excellent spatiotemporal resolution of small electrodes represents a promising methodology in bioanalytical and chemical sensing. In this paper, we report the development of reproducible electrochemical, aptamer-based (E-AB) sensors on a gold microelectrode platform. Specifically, we develop microscale sensors (25 μm diameter) for two representative small molecule targets-adenosine triphosphate and tobramycin. Furthermore, we report on the challenges encountered at this size scale including small-magnitude signals and interference from the irreversible reduction of dissolved oxygen and present methods to circumvent these challenges. Through the electrochemical deposition of dendritic gold nanostructures, we demonstrate microscale sensors with improved performance by increasing signal-to-noise and consequently sensitivity. Finally, we report on the use of the nonspecific adsorption of serum proteins as an additional layer of surface passivation for stable sensor performance. The sensor development here represents general guidelines for fabricating electrochemical, folding aptamer-based sensors on small-scale electrodes.