Urea is the most used fertilizer around the world as the main source of nitrogen to soil and plants. However, the administration of nitrogen dosage is critical, as its excess can be harmful to the environment. Therefore, the encapsulation of urea to achieve control on its release rates has been considered in several areas. In this work, encapsulation of urea by biodegradable polymer poly(3-hydroxybutyrate) (PHB) and its nanocomposites, namely PHB/MMT and PHB/OMMT, producing microcapsules by emulsion method is carried out. MMT and OMMT refer to Brazilian clays in a natural state and organophilized, respectively. In addition, the microcapsules are thus prepared to have their physicochemical characteristics investigated, then tested for biodegradation. Increment of microcapsules’ crystallinity due to the increased amount of poly(vinylacetate) (PVA), as emulsifier agent in the continuous phase, was confirmed by X-ray diffractometry (XRD) and atomic force microscopy (AFM). The presence of urea within microcapsules was verified by XRD, thermogravimetric analysis (TGA) and scanning electron microscopy (SEM). The soil biodegradation assessments showed that PHB/OMMT microcapsules present higher degradation rates in sandy soils. The overall results suggest that the composites performed better than neat PHB and are very promising; moreover, PHB/OMMT microcapsules proved to be the best candidate for the controlled-release of urea in soils.