Better managements of soil fertility are imperative for rehabilitating degraded soil in order to increase crop yields. Our objective was to assess the effect of improved fallow of different combinations of herbaceous-shrubs species and microdose of fertilizer on maize-bean yield, aboveground organic carbon sequestration and soil proprieties improvement. The treatments consisted of Pennisetum purpureum, Setaria sphacelata and Tripsacum laxum or Tithonia diversifolia combinations with 3 shrub species (Leucaena diversifolia, Calliandra calothyrsus, and Albizzia chinens) and microdoses of fertilizer (NPK-manure), two controls treatments without fertilizer were also included. These treatments were arranged in a split-plot design with, the main plot treatment consisting of herbaceous-shrubs fallow type subdivided into four subplots of beans ([M211], [NAMULENGA] [CURANTINO] and [VCB] cropped with three maize varieties [SamVita A and B], and [Gv664]. Application of microdose and herbaceous species combination increased bean and maize grain yield at both sites 21 months after trial initiation. No significant difference was observed between the different combinations in both sites and for the 3 planting seasons for assessed parameters. Herbaceous combinations increased significantly the number of nodules (P < 0.01). Highest biomass yield, C sequestration number and biomass of earthworm were found in the herbaceous-shrubs combinations treatments and lower in NPK-manure and control treatments in both sites. In addition, the number of earthworms was enhanced with application of microdose of fertilizers (546) and herbaceous-fallow grassland (725) compared to control (282) 2 years after trial initiation at Mulungu site. No significant difference was observed between the different combinations in both sites for soil temperature and moisture variation.