Atherosclerosis is a systemic disease that leads to accumulation of deposits, known as atherosclerotic plaques, within the walls of the carotids. In particular, three types of plaque can be distinguished: soft, fibrous, and calcific. Most of the computational studies who investigated the interplay between the plaque and the blood flow on patient-specific geometries used nonstandard medical images to directly delineate and segment the plaque and its components. However, these techniques are not so widely available in the clinical practice. In this context, the aim of our work was twofold: (i) to propose a new geometric tool that allowed to reconstruct a plausible plaque in the carotids from standard images and (ii) to perform three-dimensional (3D) fluid–structure interaction (FSI) simulations where we compared some fluid-dynamic and structural quantities among 15 patients characterized by different typologies of plaque. Our results highlighted that both the morphology and the mechanical properties of different plaque components play a crucial role in determining the vulnerability of the plaque.