A nanoelectrode with a controllable area was developed using commercial atomic force microscopy and a hydrogel. Although tremendous advantages of small electrodes from micrometer scale down to nanometer scale have been previously reported for a wide range of applications, precise and high-throughput fabrication remains an obstacle. In this work, the set-point feedback current in a modified scanning ionic conductance microscopy system controlled the formation of electrodes with a nanometer-sized area by contact between the boron-doped diamond (BDD) tip and the agarose hydrogel. The modulation of the electroactive area of the BDD-coated nanoelectrode in the hydrogel was successively investigated by the finite element method and cyclic voltammetry with the use of a redox-contained hydrogel. Moreover, this nanoelectrode enables the simultaneous imaging of both the topography and electrochemical activity of a polymeric microparticle embedded in a hydrogel.