Understanding how brain activity is related to animal behavior requires measuring multi-area interactions on timescales ranging from milliseconds to months. However, methods to perform long-term, electrical recordings are not optimized to record from many brain areas simultaneously. Here, we introduce the indie (independent dovetail implants for electrophysiology), a novel approach for multi-probe chronic probe implantation that enables flexible, simultaneous interrogation of neural activity from many brain regions during head restrained or freely moving behavior. The approach enables repeated retrieval and reimplantation of probes and can be combined with other modalities such as skull clearing for cortex wide optical access and optic fibers for optogenetics. Using the indie, we implanted 6 probes chronically in one hemisphere of the mouse brain and obtained stable single-unit recordings for over 1 year. The implant is lightweight, allows flexible targeting with different implantation angles, and offers enhanced stability. We validate the approach by comparing longitudinal drift and unit yield with acute recordings and irretrievably cemented probes. In a freely moving preparation, we implant up to 4 probes in freely moving mice without impacting open-field exploratory behaviors. We then performed multi-region, chronic recordings as mice learned a visual decision-making task and characterized the evolution of choice information and inter-region interactions over learning. Thus, our approach broadens the applications of chronic recording while retaining its main advantages over acute recordings (superior stability, longitudinal monitoring of activity and freely moving interrogations) and provides an appealing venue to study processes not accessible by acute methods, such as the neural substrate of learning across multiple areas.