Grain legumes form an important component for Malawi and other southern African countries' agricultural systems. They are valued mostly for their contributions to food security and soil fertility improvement. Smallholder farmers grow these legumes in diversified cropping systems whose effects on soil organic carbon and nutrient dynamics are not fully tested. Therefore, a field experiment was carried out to evaluate the effects of grain legume-based cropping systems on soil organic carbon and nutrient dynamics and trends of selected soil chemical properties down the soil profile. The experiment was implemented in Malawi at Lilongwe University of Agriculture and Natural Resources, in the Crop and Soil Sciences research farm, from 2013/14 to 2015/2016 growing season. The experiment was implemented in 2013 with seven treatments (Sole maize (Zea mays), sole maize + 92 kg N ha(-1) (MZ + 92 N), sole cowpea (Vigna unguiculata [L.] Walp), sole pigeon pea (Cajanus cajan [L.] Millsp), maize + pigeon pea (MZ + PP), maize + cowpea (MZ + CP) and pigeon pea + cowpea (PP + CP) intercrops). In 2017 soil samples were collected at depths of 0-15 cm, 15-30 cm and 30-45 cm from plots superimposed on an already established Randomized Complete Block Design (RCBD) experiment. The soil samples were then analyzed for nitrate (NO3-), ammonium (NH4+), available phosphorus (P), soil organic carbon (SOC) and pH. Soil assessment after a 3-year period shows that all legume-based cropping systems significantly improved amounts of NH4+, NO3-, available P and SOC as compared to continuous maize monocrop. The PP + CP intercrop treatment revealed significantly higher (p < 0.001) amount of NH4+ by 257.7% and 227.4% than those for MZ and MZ + 92 N, Furthermore, the PP + CP intercrop showed significantly higher (p < 0.001) amount of NH4+ than all the other legume-based cropping systems by a range of 42.2-56.9%, over sole pigeon pea and cowpea + maize intercrop, respectively. The trends were similar for NO3-, available P and SOC. The nutrients were significantly higher (p < 0.05) in the top 30 cm depth than in the lower horizons. However, no significant differences (p < 0.05) on pH were observed among treatments. From this study, it can be noted that the novel legume + legume intercrop involving pigeon pea and cowpea presents superior effects on plant nutrients' benefit and increased SOC even after some years of their previous cropping. Therefore, legume-based systems including legume + legume intercrops can form a good contribution in the quest for achieving sustainable agricultural intensification.