Little is known about the cell loading process, as the majority of tissue engineering studies focus on relatively long time points. The present study investigates the dynamic distribution of cells during the initial cell loading process in porous scaffolds, namely those made of type-I collagen and silk fibroin, with similar porosities and pore sizes. Loading efficiency of the cells was higher in the silk fibroin scaffold (90%±1.8%) compared to that in the type-I collagen scaffold (76%±1.0%). There were significantly more unattached cells in the type-I collagen scaffold at 0.5 h compared to those in the silk scaffold (p = 0.03). The number of adherent cells decreased with time in the type-I collagen scaffold (p = 0.01), whereas in the silk scaffold, the loading cells gradually attached to the biomaterials or aggregated with time. The majority of the cells gradually attached to the scaffolds within 6 h and exhibited an elongated morphology, which did not change. In general, there was no significant difference in cell adhesion and cell morphology between the two types of scaffold. The initial six hours were critical for the cell seeding process.