Integrated farming systems are sustainable strategies to intensify land productivity by combining annual crop, livestock and/or forestry activities in different spatio-temporal arrangements. Therefore, they may help tackle global food and energy insecurity and climate change in the coming decades. We investigated the effects of integrated crop-livestock (ICL) and integrated crop-livestock-forestry (ICLF) systems on quantity, quality, and origin of soil organic matter (SOM) in southeastern Brazil. A native forest and an extensive low-grazing intensity pasture system were used as references. In integrated systems, corn (Zea mays) was alternated with two consecutive years of piatã grass (Urochloa bryzantha) for cattle grazing. In ICLF, eucalyptus trees (Eucalyptus urograndis) were planted in simple rows of 15 × 2 m. Soil sampling was performed three times; in 2014, after two years of grazing; in 2015, after crop cultivation; and in 2016, after a successive grazing year, to evaluate chemical and physical composition changes of organic matter (C, N, δ13C, δ15N, and organic matter fractions) with time. Our findings showed that from 2010 to 2016, all systems (extensive grazing, ICL and ICLF) promoted increments on soil C and N stocks. However, land intensification converting extensive low-grazing intensity pasture to ICL was the most promising strategy, increasing soil C stocks at the rate of 0.28 Mg C ha−1 yr−1 from 2010 to 2016. Annual crop cultivation (corn intercropped with piatã grass) promoted high organic matter inputs on the soil, increasing the amount of soil labile organic matter fractions, which presented higher δ13C and lower δ15N values over time. SOM in the integrated farming systems was originated mainly from C4 plants. Therefore, optimizing development of piatã grass and corn increases organic residue inputs and then, soil C and N stocks. In addition, the crop period increased soil fertility parameters, which favors plant growth, thus providing high labile C inputs to the soil. In contrast, land intensification by adding the forestry component into the system (i.e., conversion from ICL to ICLF) reduced soil C (-0.22 Mg C ha−1 yr−1) and N (-0.03 Mg N ha−1 yr−1) stocks from 2010 to 2016, likely due to the reduction of C and N inputs to the soil caused by limited growth of annual crop and grass species under tree shades. In conclusion, land use intensification through ICL system contributes towards a more efficient and low-C agriculture, whereas the studied ICLF system did not bring further benefits to increase the quantity and/or quality of SOM.