Information on how bacteria in plants and soil, along with extracellular enzymes, affect nutrient cycling in Encephalartos villosus growing in nutrient-poor and acidic scarp forests is lacking. Bacteria in coralloid roots, rhizosphere, and non-rhizosphere soils were isolated to determine the potential role of soil bacterial communities and their associated enzyme activities in nutrient contributions in rhizosphere and non-rhizosphere soils. The role of soil characteristics and associated bacteria on E. villosus nutrition and nitrogen source reliance was investigated. Encephalartos villosus leaves, coralloid roots, rhizosphere, and non-rhizosphere soils were collected at two scarp forests. Leaf nutrition, nitrogen source reliance, soil nutrition and extracellular enzyme activities were assayed. A phylogenetic approach was used to determine the evolutionary relationship between identified bacterial nucleotide sequences. Twenty, twelve and seven different bacterial genera were isolated from rhizosphere, non-rhizosphere, and coralloid roots, respectively. Phosphorus and nitrogen cycling enzyme activities in E. villosus rhizosphere and non-rhizosphere soils were insignificant. More than 70% of the leaf nitrogen was derived from the atmosphere. This study revealed that plant-associated bacteria with plant growth-promoting functions, soil bacteria, and associated extracellular enzymes play a role in E. villosus nutrition and nitrogen source reliance and contribute to E. villosus rhizosphere and non-rhizosphere soil nutrition.