Electrochemical detection has a great potential in microfluidic systems due to its easy miniaturization without losing analytical performance. In addition, the use of nanomaterials in electroanalysis improves sensitivity, selectivity, and reproducibility. The topic of this review is the use of nanomaterials (nanoparticles, nanotubes, graphene) in electrochemical detection for capillary electrophoresis and microfluidic systems (microchips and paper based analytical devices). This review covers from 2015 up to now and it is a continuation of our previous review, also published in Electrophoresis journal. The following aspects of the surveyed articles are mainly addressed: type of nanomaterial, protocol of working electrode preparation (composite, drop casting and others), advantages of nanomaterial employment and application field (clinical, food, environmental and home security). The use of nanomaterials is still an interesting approach to improve the analytical performance of electrochemical detection based on microfluidic devices. Along the review, readers will find new protocols for working electrode modification, new carbon nanomaterials and promising applications in the aforementioned fields.