Diseases are major natural disturbances to forest ecosystems that cause changes to overstory tree structure and influence seedling dynamics by altering environmental conditions via functional traits. Thus, identifying the factors affecting seedling dynamics would improve the broader understanding of the seedling regeneration process after disease disturbance. We investigated 13,010 current year seedlings from 59 woody species, 44 genera, and 21 families following Japanese oak wilt disease (JOW) in 2009–2013 and 2018–2020 in a Japanese warm-temperate secondary forest. We also quantified temporal changes in canopy openness and soil moisture. Structural equation model (SEM) was used to explore the effects of environmental conditions and seedling functional traits on current year seedling density in autumn. Canopy openness gradually increased, whereas soil water content decreased throughout the study site. After 3‒5 years of disruption by JOW, the recruitment of current year seedlings increased through improvements in light conditions. The recruitment of non-current year seedlings increased after the improvement of current year seedling emergence. The functional traits of current year seedlings were likely to be affected by soil nutrients in the late JOW period, whereas litterfall production influenced the functional traits of current year seedlings in the post-JOW period. Factors affecting seedling density varied as environmental conditions changed across the JOW periods. Seedling establishment was enhanced by increased canopy openness in the late JOW period and by low litterfall, high soil nutrient content, and high soil moisture in the post-JOW period. The lack of any direct effect of seedling functional traits on seedling density might be associated with extensive changes in abiotic conditions caused by JOW disturbance. Our study provides evidence that the temporal changes in environmental conditions and seedling densities occurring after disruption by JOW differed from the changes in forests impacted by other natural disturbances.