Analysis of a large number of samples by electrochemical methods for rapid optimization of amperometric biosensors or screening applications is still a challenge. To overcome this limitation, a system with 96 screen-printed electrodes was developed to assay H2O2 produced by free and immobilized galactose oxidase as a model for oxidases. Detection was based on two electrochemical methods: intermittent pulse amperometry (IPA) and electrochemiluminescence (ECL). This 96-well electrochemical device allowed rapid optimization of the parameters in half a day, regardless of the method used (i.e., IPA or ECL). We demonstrate that ECL is more sensitive for the detection of H2O2 (limit of detection of 1 μm for ECL vs. 10 μm for IPA) with lower interelectrode variability (1 vs. 19 %). Rapid determination of sensitivities, linear ranges, and limits of detection of galactose oxidase substrates (e.g., dihydroxyacetone and l-erythrulose) by using free or immobilized enzyme was conducted in only 50 min by the mean of 5 different sets of 96 screen-printed electrodes.