Proper health management is essential for productivity in duck farming. However, there is limited information on the effect of management conditions on rates of metabolic problems and parasitic infections in anatids. We evaluated the rates of metabolic syndromes and gastrointestinal parasite involvement in Muscovy ducks up to 12 weeks of age, under 3 management conditions: backyard, organized, and organized with probiotics. Individuals under organized management developed 2 metabolic problems: ascites, which was rare (3.5%), fatal, and affected both males and females, and angel wing syndrome, which was more frequent (10.6%), has low impact on general health, and only affected males. The treatments do not have a significant effect on the development of ascites, but only individuals in controlled conditions presented this syndrome, and due to its low prevalence, further studies with a larger sample size are required. The risk of angel wing syndrome increased significantly with probiotic supplementation. Regarding to parasitic infection, the improvement of sanitary management and the use of probiotics supplementation reduced the occurrence of coccidiosis. Similarly organized management with probiotic supplementation showed a protective effect on helminthiasis by reducing the frequency of Heterakis gallinarum and greatly reducing the helminth egg load. Coccidiosis and helminthiasis infections were not significantly correlated with the final weight of the ducks. Therefore, organized management and the use of probiotics seems to reduce the impact of parasitic infection, although it increases the risk of developing metabolic syndrome.