Continual monitoring of secreted biomarkers from organ-on-a-chip models is desired to understand responses to drug exposure in a noninvasive manner. To achieve this goal, analytical methods capable of trace amounts of secreted biomarkers are of particular interest. However, a majority of existing biosensing techniques from limited sensitivity, selectivity, stability, and require large working volumes, especially when cell culture medium is involved, which usually contains a plethora of nonspecific binding proteins and interfering compounds. Hence, novel analytical platforms are needed to provide noninvasive, accurate information on the status of organoids at low working volumes. Here, we report a novel microfluidic aptamer-based electrochemical biosensing platform for monitoring damage to cardiac organoids. The system is scalable, low-cost, and compatible with microfluidic continued.