Simple SummaryNosema ceranae is a highly prevalent intracellular parasite of honey bees’ midgut worldwide. There is a lack of studies addressing the influence of climatic and beekeeping factors on the dynamics of its infection. A long-term study has been carried out in six apiaries in four Mediterranean countries (France, Israel, Portugal, and Spain), monitoring a total of 103 colonies. The lowest prevalence of infection was observed in mainland France, while the highest percentage of infected honey bees per colony was detected in Israel. The location and beekeeping management were shown to influence the infection levels. The percentage of infected honey bees negatively affected the colony strength in the apiaries located in Spain and mainland Portugal, whereas queen replacement had a positive effect on these same apiaries, reducing infection levels. The highest colony losses occurred in mainland France, which had the lowest levels of N. ceranae. It was followed by Spain, an apiary with high levels of N. ceranae, so no correlation between infection and mortality could be established. These results suggest that complementary studies on interactions with other pathogens and honey bee genetics are needed in order to develop management strategies for its control.Nosema ceranae is a highly prevalent intracellular parasite of honey bees’ midgut worldwide. This Microsporidium was monitored during a long-term study to evaluate the infection at apiary and intra-colony levels in six apiaries in four Mediterranean countries (France, Israel, Portugal, and Spain). Parameters on colony strength, honey production, beekeeping management, and climate were also recorded. Except for São Miguel (Azores, Portugal), all apiaries were positive for N. ceranae, with the lowest prevalence in mainland France and the highest intra-colony infection in Israel. A negative correlation between intra-colony infection and colony strength was observed in Spain and mainland Portugal. In these two apiaries, the queen replacement also influenced the infection levels. The highest colony losses occurred in mainland France and Spain, although they did not correlate with the Nosema infection levels, as parasitism was low in France and high in Spain. These results suggest that both the effects and the level of N. ceranae infection depends on location and beekeeping conditions. Further studies on host-parasite coevolution, and perhaps the interactions with other pathogens and the role of honey bee genetics, could assist in understanding the difference between nosemosis disease and infection, to develop appropriate strategies for its control.