This study is designed to investigate the impact of chemical properties of soil on spore density, colonization, and distribution of native arbuscular mycorrhizal (AM) fungal species associated with chillies (Capsicum annuum L.) from six sites in Phaltan tehsil of Satara District, Maharashtra, India. The AM fungi spore density and root colonization were positively correlated with pH (r = 0.470 and r = 0.246, respectively), organic carbon, N, Zn, Cu, and free lime, while they were negatively correlated with P (r = −0.025 and r = −0.148, respectively), K, and Na. The soil EC (r = 0.346 and r = −0.064, respectively), Fe, and Mn were positively correlated with spore density and were negatively correlated with root colonization. Out of the 52 species of native AM fungi identified, Glomus was the most frequently (55%) occurring genus with 29 species, followed by Acaulospora with 13 species and Scutellospora with 6 species. Gigaspora (5.7%) and Entrophospora (1.9%) were the least occurring genera with three and one species, respectively. The influence of soil factors on the occurrence and distribution of native AM fungi was also studied from the six selected sites. Our findings highlight the relationship between soil nutrients and AM fungi, and hence provide insight into the potential use of the combination of native species of AM fungi for the cultivation of chillies and other crops.