Molluscs, characterised by various shapes and sizes, represent the most diverse group of animals after arthropods. This morphological disparity has historically complicated the establishment of phylogenetic relationships among the different classes of molluscs and subclasses of gastropods and their positions within the lophotrochozoans. In recent decades, ultraconserved elements (UCEs) have emerged as an effective technique for capturing large numbers of genes from preserved museum specimens across various animal groups. This study evaluates the efficiency of UCE capture across all classes of molluscs using a probe set designed for heterobranch gastropods. We analysed the effects of missing data using three levels of the GBLOCKS masker, ZORRO, and by generating various occupancy matrices. Our analyses successfully captured 2,119 out of 2,259 possible UCEs, recovering many genes from all molluscan classes and gastropod subclasses (144–1,604). As expected, efficiency decreases in groups more distantly related to gastropods, particularly heterobranchs. The more stringent maskers recovered shorter sequences with less missing data, yet fewer informative sites. Thus, our primary analyses focused on the use of more relaxed masking settings and the 50% occupancy matrix. These analyses resolved the well-established Conchifera and Aculifera hypothesis and further recovered a close relationship between Bivalvia and Scaphopoda (Diasoma). Moreover, with a wider taxon sampling, the interrelationships within, e.g., Gastropoda and Solenogastres are well resolved, highlighting the true universality of the probe set and encouraging its use for future research on any mollusc class.