The major prerequisite for the clinical application of intracortical microelectrodes, or any other neural implant, is that the organism accepts them without causing an unacceptable degree of harm. However, all biomaterials, even those thought to be highly biocompatible, provoke a biological response and some degree of encapsulation. This means that the body can tolerate them, although they are not fully compatible. Therefore, a significant goal is to improve the knowledge and understanding of the interaction between the implanted devices and the local cellular environment in order to improve the long‐term biotolerability, applicability, and functional perspectives of intracortical microelectrode arrays. In this article, some of the main challenges in this field that involves biomaterials science, bioengineering, neurology, neurosurgery, and neuroscience research are discussed.