Single-walled carbon nanotube press-transferred electrodes (SWPTEs) are new disposable electrodes where carbon nanotubes act as exclusive electrochemical transducers, being an excellent alternative to common approaches in the field. In the current work, these pioneering SWPTEs coupled to microfluidic chips (MCs) have been employed to develop their first real application. A class-selective electrochemical isoflavone index determination has been proposed for fast and reliable qualitative and quantitative assessment of class-isoflavones based on the co-migration of the total glycosides (TG) and total aglycones (TA) in less than 250 s with very good intra-SWPTE repeatability (RSDs ≤ 8%, n = 5) and inter-SWPTE reproducibility (RSDs ≤ 9%, n = 3). These novel SWPTEs are entering with important roles into the micro and nanotechnology scenes expanding new frontiers in the food analysis and health field.