Intensive urban agriculture is expanding in Cameroon, which increases the risks of environmental pollution, particularly in the lowlands. This study assessed the seasonal characteristics of some potentially toxic elements and their ecological risks during the dry and wet seasons in urban agricultural soils in four lowlands in Yaoundé. The area and seasonal variation of some potentially toxic elements (Cu, Pb, Zn, Cd, Cr, and Ni) were evaluated using mixed-effects modeling. The pollution status of these elements in the soil was evaluated and interpreted using parameters such as the single pollution (SPI) and Nemerow composite pollution (NCPI) indices. In addition, the effect of these metals in the environment was assessed using the potential ecological risk index (PERI). The distribution of all the studied elements showed an area effect, while a seasonal effect was only noticeable for Cu. The concentration of Cu, Pb, and Zn was higher than the recommended threshold values in one of the areas sampled, while Cr exceeded these threshold values in all areas during both seasons. Cr exhibited the highest SPI among all studied elements during the dry and wet seasons in all areas. Except for the NCPI in one area, where grade V (strong) soil pollution was recorded during the wet season, the soil from all the study areas exhibited a slight pollution level (grade III) with a mean NCPI between 1 and 2. The PERI value of all areas was below the reference values during both seasons, suggesting an overall low potential contamination risk of the soil biota. The results indicate that preventive action to limit the heavy metal contamination in the lowlands of Yaoundé needs to be taken, for instance, through the promotion of more sustainable use of agrochemicals like pesticides and mineral fertilizers.