Environmental DNA (eDNA) metabarcoding of floral samples has emerged as a valuable tool for characterizing pollinator communities and plant–pollinator interactions. However, commonly used universal arthropod primers often fail to consistently recover bee (Apiformes) DNA from mixed-template samples. To overcome this limitation, a new COI metabarcoding primer pair specifically designed for bees was developed: BeePrimeF and BeePrimeR. In silico evaluations and in vitro assays demonstrated high target specificity, with only limited amplification of non-target taxa. When applied to floral eDNA from Austrian flower strips, the BeePrime primers doubled the number of samples testing positive for bees and substantially increased the detected bee diversity. Individual floral samples typically yielded multiple bee species rather than single detections, and across all samples, BeePrime detected more than four times as many distinct bee species as a commonly used universal primer. In addition, BeePrime produced significantly higher proportions of bee reads per sample, thereby improving sequencing efficiency and data quality. All molecular identifications were corroborated by specimen-based surveys conducted at the same sites and validated through morphological identification. Overall, BeePrime overcomes a key methodological bottleneck in pollinator eDNA metabarcoding and substantially strengthens the molecular toolkit available for monitoring bee diversity and resolving plant–pollinator networks.