The research relevance is determined by the decline of bee populations in Albania, as the need to understand the dynamics of colony loss and the factors contributing to it is of paramount importance. The study aimed to comprehensively investigate the prevalence and main causes of colony losses, with special attention to Varroa mite infestation, Nosema disease, viral pathogens, pesticides, and bacterial infections. Using the stratified sampling method, 15,493 beekeepers of different ages and experiences participated in the study. Both electronic and face-to-face surveys were used to collect data on bee family losses, management practices and environmental factors affecting bee health. In addition, monitoring programmes allowed a detailed assessment of bee family health and environmental conditions in the apiary, providing valuable information on temporal trends and patterns. The findings indicate alarming rates of Varroa mite infestation, prevalence of Nosema and a complex interplay of factors contributing to colony loss, particularly during the summer and winter months. For example, Varroa mite infestation was found in 61% of the 29,474 bee samples collected during summer sampling, with rates ranging from 0.5% to 70.2%. Similarly, during autumn sampling, 65% of 43,037 bee samples contained Varroa mites, with an average infestation rate of 5.3%. Moreover, Nosema disease is also a complex problem, with clinical prevalence ranging from 0.1% in autumn to 1.3% in summer and spring. These key figures highlight the urgent need to develop effective strategies to reduce Varroa mite infestation and Nosema disease, thereby maintaining bee populations and ecosystem health. The results of the study make a valuable contribution to bee management and policy development, emphasising the importance of holistic approaches to maintaining bee health and resilience in Albania