Intercropping cover crops with trees enhance land productivity and improves the soil’s
physio-chemical properties while reducing the negative environmental impact. However, there is a
lack of quantitative information on the relationships between fine root biomass and available soil
nutrients, e.g., nitrogen (N), phosphorus (P), and potassium (K), especially in the rubber-Flemingia
macrophylla intercropping system. Therefore, this study was initiated to explore the seasonal variation
in fine root biomass and available soil nutrients at different stand ages (12, 15, and 24 years) and
management systems, i.e., rubber monoculture (mono) and rubber-Flemingia macrophylla intercrop-
ping. In this study, we sampled 900 soil cores over five seasonal intervals, representing one year
of biomass. The results showed that the total fine root biomass was greater in 12-year-old rubber
monoculture; the same trend was observed in soil nutrients P and K. Furthermore, total fine root
biomass had a significant positive correlation with available N (p < 0.001) in rubber monoculture
and intercropping systems. Thus, it suggests that fine root growth and accumulation is a function
of available soil nutrients. Our results indicate that fine root biomass and soil nutrients (P and K)
may be determined by the functional characteristics of dominant tree species rather than collective
mixed-species intercropping and are closely linked to forest stand type, topographic and edaphic
factors. However, further investigations are needed to understand interspecific and complementary
interactions between intercrop species under the rubber-Flemingia macrophylla intercropping system.