Dicyandiamide (DCD) has been studied as a stabilizer for nitrogen fertilizers for over 50 years. Its efficacy is limited at elevated temperatures, but this could be addressed by encapsulation to delay exposure. Here, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) was investigated as a biodegradable matrix for the encapsulation of DCD. Cylindrical ∼3 mm × 3 mm pellets were fabricated through extrusion processing with 23 wt % DCD. Release kinetics were monitored in water, sand, and both active and γ-irradiated agricultural clay loam soils. Raman maps showed a wide particle size distribution of DCD crystals and indicated that Hitachi’s classic moving front theory did not hold for this formulation. The inhibitor release kinetics were mediated by four distinct mechanisms: (i) initial rapid dissolution of surface DCD, (ii) channeling of water through voids and pores in the PHBV matrix, (iii) gradual diffusion of water and DCD through layers of PHBV, and (iv) biodegradation of the PHBV matrix. After ∼6 months, 45–100% release occurred, depending on the release media. PHBV is shown to be an effective, biodegradable matrix for the long-term slow release of nitrification inhibitors.