Confinement is common in biological systems and plays a critical role in the structure-forming process of biominerals. However, the knowledge of confinement effects on biomineralization is limited due to the lack of specific chemical structures and elaborate spatial distribution. In this article, we explore the confined mineralization of amorphous calcium carbonate (ACC) within collagen fibrils. Three issues of the confined mineralization of ACC within collagen fibrils were investigated, including the morphology and characteristics of the confined mineralization of ACC within collagen fibrils; the initiation and development of the confined mineralization of ACC within collagen fibrils; and the driving mechanism of ACC infiltration into collagen fibrils. Results show that the negatively charged ACC droplets were attracted to positively charged gap regions of collagen fibrils through electrostatic interactions, infiltrated into collagen fibrils, and then transformed into the crystalline phase. The observation of juxtaposed crystalline and amorphous phases on the surface of fibrils indicates that a secondary nucleation mechanism may be responsible for the co-orientation of calcite nanocrystals. Through modifying the wettability of amorphous calcium carbonate with magnesium ions, it is verified that the infiltration of ACC into collagen fibrils was driven by capillary forces. The present study not only provides evidence of the confinement effects in biomineralization but also facilitates the understanding of the in vivo bone formation process. It may also open up a new avenue in the bioprocess-inspired synthesis of advanced materials.