The use of micro- and nanomaterials as carriers of therapeutic molecules can enhance the efficiency of treatments while avoiding side effects thanks to the development of controlled drug delivery systems. The binding of a dye to a drug or to a drug carrier has opened up a wide range of possibilities for an effective in vivo optical tracing of drug biodistribution by using non-invasive real-time technologies prior to their potential use as therapeutic vectors. Here, we describe the fluorescent tagging of polymeric micro- and nanomaterials based on poly(lactic-co-glycolic) acid and on the thermoresponsive poly(N-isopropylacrylamide) with the fluorescent probe IR-820 which was chemically modified for its covalent coupling to the materials. The chemical modification of the dye and the polymers yielded micro- and nanoparticulated labelled materials to be potentially used as drug depots of different therapeutic molecules. In vitro biological studies revealed their reduced cytotoxicity. A spatiotemporal in vivo micro- and nanoparticle tracking allowed the evaluation of the biodistribution of materials showing their local persistence and high biocompatibility after pathological studies. These results underline the suitability of these materials for the local, sustained, not harmful and/or on-demand drug delivery and the remarkable importance of evaluating the biodistribution of materials and tissue persistence for their use as local drug depots.