Abstract Cell seeding on 3D scaffolds is a very delicate step in tissue engineering applications, influencing the outcome of the subsequent culture phase, and determining the results of the entire experiment. Thus, it is crucial to maximize its efficiency. To this purpose, a detailed study of the influence of the geometry of the scaffold fibers on dynamic seeding efficiency is presented. 3D printing technology was used to realize polylactic acid porous scaffolds, formed by fibers with a non-circular cross-sectional geometry, named multilobed to highlight the presence of niches and ridges. An oscillating perfusion bioreactor was used to perform bidirectional dynamic seeding of MG63 cells. The fiber shape influences the fluid dynamic parameters of the flow, affecting values of fluid velocity and wall shear stress. The path followed by cells through the scaffold fibers is also affected and results in a larger number of adhered cells in multilobed scaffolds compared to scaffolds with standard pseudo cylindrical fibers. Geometrical and fluid dynamic features can also have an influence on the morphology of adhered cells. The obtained results suggest that the reciprocal influence of geometrical and fluid dynamic features and their combined effect on cell trajectories should be considered to improve the dynamic seeding efficiency when designing scaffold architecture.