In this paper, the effects of prolonged bias-enhanced nucleation ("prolonged BEN") on the growth mechanisms of diamond are investigated by molecular dynamics (MD) and combined MD-Metropolis Monte Carlo (MD-MMC) simulations. First, cumulative impacts of C(x)H(y)(+) and H(x)(+) on an a-C:H/nanodiamond composite were simulated; second, nonconsecutive impacts of the dominant ions were simulated in order to understand the observed phenomena in more detail. As stated in the existing literature, the growth of diamond structures during prolonged BEN is a process that takes place below the surface of the growing film. The investigation of the penetration behavior of C(x)H(y)(+) and H(x)(+) species shows that the carbon-containing ions remain trapped within this amorphous phase where they dominate mechanisms like precipitation of sp(3) carbon clusters. The H(+) ions, however, penetrate into the crystalline phase at high bias voltages (> 100 V), destroying the perfect diamond structure. The experimentally measured reduction of grain sizes at high bias voltage, reported in the literature, might thus be related to penetrating H(+) ions. Furthermore, the C(x)H(y)(+) ions are found to be the most efficient sputtering agents, preventing the build up of defective material.