The effects of Irvingia fruit wastes on soil microbial diversity and physico-chemical properties were assessed through metagenomics and chemical analyses. Topsoil was thoroughly homogenized and separated into three different groups (Treatments 1, 2 and 3 soils respectively). Treatment 1 soil samples were assessed without any further processing. Treatment 2 soil samples were incubated for 14 days at ambient temperature and assessed whilst Treatment 3 soil samples were amended with Irvingia fruit wastes and incubated for 14 days at same temperature. Results showed that microbial diversity, total sequence reads, Operational Taxonomic Units (OTUs) and soil physico-chemical properties were influenced by Irvingia fruit wastes. Bacterial diversity for Treatments 1, 2 and 3 soils were 0.90, 0.28 and 0.93, respectively whilst bacterial total sequence reads and OTUs amplified from Treatment 1, 2 and 3 soils were 3,040 (82 OTUs), 23,544 (87 OTUs) and 16 (10 OTUs), respectively. Fungal diversity for same soil samples were 0.95, 0.80 and 0.33, respectively. Fungal total sequence reads and OTUs were 4,394 (50 OTUs), 55 (13 OTUs)