The microstructural evolution of UNCD films which are P-ion implanted and annealed at 600 °C (or 800 °C) is systematically investigated. The difference of interaction that the UNCD content undergoes along the trajectory of the incident P-ions is reflected in the alteration of the granular structure. In regions where the P-ions reside, the “interacting zone,” which is found at about 300 nm beneath the surface of the films, coalescence of diamond grains occurs inducing nano-graphitic clusters. The annealing at 600 °C (or 800 °C) heals the defects and, in some cases, forms interconnected graphitic filaments that result in the decrease in surface resistance. However, the annealing at 600 °C (800 °C) induces marked UNCD-to-Si layers interaction. This interaction due to the annealing processes hinders the electron transport across the interface and degrades the electron field emission properties of the UNCD films. These microstructural evolution processes very well account for the phenomenon elaborating that, in spite of enhanced conductivity of the UNCD films along the film's surface due to the P-ion implantation and annealing processes, the electron field emission properties for these UNCD films do not improve.