The increasing interest in sustainable methods in agroforestry directs the attention of many to arbuscular mycorrhizal fungi (AMF) for their role in maintaining or improving overall plant health and nutrition of many plants including cacao (Theobroma cacao L.) trees. The effects of different treatments of AMF and other soil amendments applied singly or in combination on physicochemical properties, nutrient levels, spore count, and rhizosphere microbial counts, were investigated and compared across different sampling periods of varying climatological conditions in an agroforest system. Results showed that there was a significant effect on the N content using the different treatments. The treatment using AMF from MR (MYKORICH) alone has the highest N level (%) (0.587 ± 0.024, p < 0.001). Levels of P (ppm) and K (cmolc/kg) and soil physicochemical properties were not significantly affected by AMF applications. N levels were highest in January (1.772 ± 0.018, p = 0.004) which was the same month recorded with the lowest P content (0.0163 ± 2.228, p < 0.0001). Soil physicochemical properties did not significantly vary between sampling periods except for organic matter (OM) which was highest in October (2.883 ± 0.151, p = < 0.001), and with water-holding capacity (WHC) in March (80.429 ± 1.775, p 0.0001) and between the sampling months (p < 0.0001). Results showed that the effect of season on spore count was not the same for each of the treatments used and vice versa (p = 0.001). Microbial counts on nitrogen-fixing bacteria and phosphate-solubilizing bacteria showed no variability between treatments (p = 0.134). These findings guide cacao farmers in directing future interventions for improving soil conditions and yield in cacao agroforests.