Calcific aortic valve disease (CAVD) is an active progressive disease characterized by calcification of the aortic valve, causing tissue stiffening and eventually valve malfunction. As an age-related disease, CAVD has become a rising public concern due to improved healthcare and longevity. However, the lack of understanding of the disease's progression and mechanism remains unclear, limiting the development of pharmacologic treatments. Here, we aim to understand how the morphology of hydroxyapatite in a mineral-rich matrix can affect the behavior of valve cell populations in a model for later disease stages. By incorporating hydroxyapatite nanoparticles and mineralized collagen fibrils into the in vitro 3D hydrogel model that mimics the aortic valve microenvironment, we were able to observe the lesion formation, its chemical composition and spatial distribution with Raman mapping, and cell behavior through a histology approach.