Despite the burgeoning number of non-indigenous species (NIS) in worldwide coastal ecosystems, the quantification of their direct impacts on native communities remains largely unexplored. This is particularly true concerning feeding competition in sympatric filter-feeding bivalves. In this study, our aim was to fill a gap of knowledge on the potential trophic competition between native and non-indigenous bivalves, namely by focusing on three species that co-occur in Portuguese estuarine systems: the native cockle (Cerastoderma edule) and Portuguese oyster (Magallana angulata) and the non-indigenous Manila clam (Ruditapes philippinarum). The specific objectives were to i) estimate their capture efficiency (≈ particle retention efficiency; CE); ii) assess their clearance rates (CR); and iii) provide a science-based support for suitable management measures regarding NIS. Experiments were conducted in both field and laboratory conditions using the natural seston present in the seawater. The CE was higher for the larger size classes (8–14 μm) of particles measured (ranging from 4–14 µm), regardless of the species. While the individual CRs were not significantly different among species, the CR per gram of ash-free dry body tissue weight was significantly higher for the native cockle, suggesting that the NIS does not hold a competitive advantage in clearing suspended particles. However, the Manila clam might be limiting food sources availability to the native species since there is an overlap of their ecological niches.