The seabed rarely consists solely of bare sand: often other materials, such as shells are present. They can influence sand transport by armoring the bed and modifying its roughness. Biogenic shells come in different shapes and sizes, depending on the mollusc species that produce them. To understand how changes in bivalve species composition affect sediment transport, we need a mechanistic understanding of how shell content and shell shape influence the near-bed flow and sand transport. We performed experiments in a racetrack flume, testing the effect of elongated (Ensis leei) versus rounded (Spisula subtruncata) shells on unidirectional current-driven sand transport. For both types of shells, a higher depth-averaged flow velocity was needed for initiation of motion and a decrease in bedload transport of sand was found. At a shell content of 20%, the threshold of motion of sand increased up to 75%, and bedload transport was reduced by up to 50%. These effects are explained by a balance between roughness-induced turbulence and bed armoring. Compared to a bare bed, shells decreased bed roughness by reducing ripple formation; rounded shells lowered roughness more than elongated shells, which formed roughness elements themselves, but also covered a larger fraction of the bed. However, there was no clear difference between round versus elongated shells on the overall sand transport; only shell content was key for the overall effect. Our results imply that sediment transport is likely overpredicted when a high number of shells is present in the seabed.