We report here the fabrication and the electrochemical characterization of recessed disk microelectrodes (rDME) and ring nanoelectrodes (rRNE) integrated into microwell arrays. The technological process based on the reactive ion etching of a SiO2/Ti/Pt/Ti/SiO2 stack is optimized in order to realize functional electrochemical microdevices on glass substrate and so, enable the coupling of amperometric measurements with optical analysis. Multiphysic simulations and electrochemical characterizations are carried out to study and enhance the amperometric performance of recessed ring nanoelectrodes arrays (rRNEA) according to their geometry. Finally, all these results demonstrate that rRNEA are fitted for the detection of bio-electrochemical species at the microscale and consequently, for the analysis of the metabolic status of isolated mitochondria through the measurement of dissolved oxygen and hydrogen peroxide.