This study was undertaken to determine long-term soil organic matter (SOM) accumulation dynamics from added mango leaf litter (MLL) into tilled (MT) and non-tilled soil (MnT) through integrated field experiment (bio-physico-chemical edaphic properties) and system dynamics modeling. Field data shows that the coarse (Lf) and fine (Fn) fractions of SOM have no significant difference (p > 0.05) between MT and MnT during the dry season. In contrast, there is a significant difference (p < 0.01) in the Fn fraction between MT and MnT during the wet season. The total N, available P, exchangeable K, as well as the collembola, bacteria, and fungi in the soil were also assessed. Of these parameters, the available P and exchangeable K have a significant difference between the MnT and MT during the dry season. In comparison, the total N and collembola significantly differed during the wet season. The results of the field experiment were used in the parametrization to build the SOM accumulation model. The 20-year simulation showed that the incorporation of MLL into the soil through tillage increased SOM from 3.09% to 3.13%, with an average of 2.78 ± 0.018%. In the non-tilled orchard, SOM also increased from 3.09% to 4.23%, with an average of 3.59 ± 0.035%. This SOM level can sustain the fertility and productivity of the mango agroecosystem. The increase in SOM is accounted for by the coarse fraction both in tilled and non-tilled plots. Given the foregoing, with minimum tillage, mango orchards can be developed into crop-based systems.