<p><i>Nosema ceranae,</i> a widely distributed microsporidium, is one of the major factors contributing both to colony loss and to the impairment of <i>Apis mellifera</i> health. Studies on its prevalence have been limited to national levels, and have shown wide variability, probably in response to various factors, but it is unclear which represent risk factors. To address these gaps, a systematic review and meta-analysis was conducted to estimate the global and regional prevalence of <i>N. ceranae</i> infection in colonies and apiaries of the European honey bee, and explored associated risk factors. Following PRISMA guidance, literature searches in Web of Science, PubMed, Scopus and SciELO identified 48 cross-sectional studies meeting predefined eligibility criteria on language, design, outcome definition and reporting, with risk of bias assessed using the Newcastle–Ottawa Scale adapted for cross-sectional studies. The meta-analysis showed a combined overall prevalence of 39.52% (95%CI: 29.01; 50.51) at the colony level, with Northern America having the highest combined prevalence. At the apiary level, it was 34.93% (95%CI: 27.23; 43.00), with Europe being the region with the highest levels. Climate type explained between-study heterogeneity: tropical and temperate climates increased colony-level risk, whereas temperate and arid climates increased apiary-level risk.</p>