Doping of silicon nanocrystals (Si-NCs) is one of the major challenges for silicon nanoscale devices. In this work, phosphorus (P) doping in Si-NCs which are embedded within an amorphous silicon matrix is realized together with the growth of Si-NCs by plasma-enhanced chemical vapor deposition under a tunable substrate direct current (DC) bias. The variation of phosphorus concentration with substrate bias can be explained by the competition of bonding processes of Si-Si and P-Si bonds. The formation of Si-Si and P-Si bonds is differently influenced by the ion bombardment controlled by the substrate bias, due to their bonding energy difference. We have studied the influences of grain size on P doping in Si-NCs. Free carrier concentration, which is provided by activated P atoms, decreases with decreasing grain size due to increasing formation energy and activation energy of P atoms incorporated in Si-NCs. Furthermore, we have studied the P locations inside Si-NCs and hydrogen passivation of P in the form of P-Si-H complexes using the first-principles method. Hydrogen passivation of P can also contribute to the reduced free carrier concentration in smaller Si-NCs. These results provide valuable understanding of P doping in Si-NCs.