<p>Vascular Fusarium wilt and floral virescence are two significant diseases affecting cotton production in Côte d’Ivoire, leading to substantial crop losses. Current knowledge regarding the distribution of these diseases is limited as most existing studies are outdated. Consequently, there is a need for updated data to assess the evolution of these diseases in cotton-growing regions. This study aimed to investigate the spatial and temporal occurrence of these diseases by examining 600 small farms between 2022 and 2024. The incidence of Fusarium wilt varied among cropping seasons, with no statistically significant differences observed (<i>p</i> = 0.351). The highest incidence was recorded in 2022, with peaks of 0.023% in late July, 0.020% in mid-August, and 0.066% in mid-September, followed by a complete decline at the end of the cropping cycle. During the 2023 and 2024 seasons, Fusarium wilt incidence remained very low, ranging from 0 to 0.01%. Regarding floral virescence, a similar seasonal pattern was observed across the three years, with disease onset occurring in late July. The highest incidence was observed in 2022, peaking at 0.25% in early September. Interannual variation in virescence incidence was statistically significant (<i>p</i> = 0.007). Spatially, Fusarium wilt was mainly concentrated in the southern part of the cotton-growing basin, with a progressive extension toward central areas. In contrast, floral virescence was predominantly observed in the northern basin, with a gradual spread toward central and southern localities. A highly significant geographical effect was recorded (<i>p</i> &lt; 0.001). These results highlight the need to implement targeted phytosanitary strategies, including vector control and introduction of resistant cotton varieties. They may also guide the selection of plots for seed production.</p>