The Nutmeg tree (Myristica fragrans Houtt.) serves as a Multi-Purpose Tree Species (MPTS) in high demand due to its multitude of applications. Despite its potential, Indonesia's nutmeg productivity lags behind the global average, with a yield of only 98.9 kg per hectare. Among the various impediments to productivity, the limited expertise of local farmers in nutmeg cultivation and the prevalence of leaf diseases in nutmeg seedlings in nurseries are paramount. Leaf diseases can be lethal to the seedlings and significantly impact their quality, which, in turn, affects the growth and productivity of the mature plants. This study was conducted to assess the prevalence of leaf diseases in nutmeg nurseries and identify the causal pathogens. The average percentage of damage across all disease types was found to be as follows: leaf spot (3.95%), leaf blight (4.42%), leaf rust (7.27%), and powdery mildew (1.025%). Pathogenic fungi were identified as the causative agents, with Nigrospora sp. causing leaf spot, Rhizoctonia sp. causing leaf blight, Oidium tingitanium causing powdery mildew, and Pestalotia sp. causing leaf rust. The overall average intensity of pathogen attack was 6.52%, classified in the mild damage category. Our findings suggest that fungal pathogens predominantly cause leaf diseases in nutmeg seedlings. Therefore, effective microclimate management strategies should be adopted to mitigate the impacts of these diseases in nutmeg nurseries.