Expansion and intensification of agricultural land in the tropics increasingly raises environmental concerns and questions about sustainability of production systems. A key parameter to consider when assessing the sustainability of production systems is soil fertility, and of particular interest are macronutrients, pH, electrical conductivity, and microbial communities. To understand which environmental factors influence soil fertility, we studied the abovementioned key parameters in two agroforestry systems (rustic and polyculture) in Bali, Indonesia. Via Generalized Linear Models, we found that agroforestry system, canopy cover, crop richness, tree richness, and yields had differing effects on topsoil (0–5 cm) and subsoil (10–15 cm) properties, including C:N ratios, conductivity, K, organic C, P, and total microbes. We found a higher C:N ratio in topsoil (p = 0.027), higher organic carbon content in topsoil (p = 0.009) and subsoil (p < 0.001), higher total microbes in subsoil (p = 0.001), and lower phosphorus levels in topsoil (p < 0.001) in rustic than in polyculture systems. Rustic systems may foster conditions conducive to soil fertility, and in our study, canopy cover (p < 0.001) and tree richness (p < 0.001) emerge as a key positive drivers of the total number of microbes in topsoil. The positive associations observed between crop and tree richness with electrical conductivity and total microbe counts underscore the importance of biodiversity in enhancing soil fertility, emphasizing the need for diversified agricultural systems to promote soil fertility. With soil fertility declining across the world due to global investments in agricultural intensification, it is vital that food production systems divert to the use of systems such as agroforestry in order to ensure soil sustainability and food security for future generations.
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