Recent advocacy for Integrated Soil Fertility Management (ISFM) in smallholder farming systems in east and southern Africa show substantial evidence of increased and sustained crop yields associated with enhanced soil productivity. However, the impact ISFM on soil fungi has received limited attention, yet fungi play key roles in crop growth. Following total soil DNA extraction with ZR soil microbe miniprep kit, illumina sequencing was used to, examine the fungal communities (ITS1F) under a maize crop following co-application of organic nutrient resources including Crotalaria juncea, cattle manure and maize stover with inorganic fertilizers at three-time periods (T1-December, T2-January, and T3-February) in Zimbabwe. Ninety-five fungal species were identified that were assigned to Ascomycota (>90%), Basidiomycota (7%) and Zygomycota (1%). At T1, Ascomycota and Basidiomycota were identified across treatments, with Ascomycota attaining > 93% frequency. Fungal succession was noted and involved reduction of Ascomycota coupled by increase in Basidiomycota under the different treatments. For example at T3, Basidiomycota increased to 34% while Ascomycota declined to 66% under manure but remained unchanged in other two organics. Pre-season mineral nitrogen (N) associated with the 'Birch effect' apparently influenced the fungal community structure at T1 while readily available fertilizer N was critical at T2 and T3. The low-quality maize stover promoted the presence of Exophiala sp SST 2011 and this was linked to N immobilization. The impact of N addition was more pronounced under medium (manure) to low-quality (maize stover) resources. Fungi required phosphorus (P) and N for survival while their proliferation was dependent on substrate availability linked to resource quality. Interactive-forward test indicated that soil available P and N were most influential (P < 0.05) factors shaping fungal communities. Co-application of medium to high quality organic and inorganic resources show promise as a sustainable entry point towards enhancing belowground fungal diversity critical in driving nutrient supply.