The continued decline in both populations and diversity of soil macrofauna in agroecosystems remains a major concern for sustainable food production in Southern Africa. Macrofauna abundance and diversity were examined in a maize monocropping system following repeated incorporation of Calliandra calothyrsus, Crotalaria juncea, cattle manure, maize stover, and Pinus patula sawdust at 1.2 or 4.0 t C ha−1 with or without nitrogen (120 kg N ha−1) for 13 years (seasons). All treatments received phosphorus (P), potassium (K), and sulphur (S) at 16.0, 14.7 and 4.6 kg ha−1, respectively, at each planting time in December. Using the ISO/TSBF (Tropical Soils Biology and Fertility Institute) monoliths procedure, macrofauna were collected to a depth of 0.30 m fortnightly from February to mid-May 2016. Lumbricus terrestris and Isoptera were significantly (P < 0.001) affected by organic treatment and seasonal time, while organic treatment alone significantly affected Elateridae. A fluctuating trend characterised Diplopoda, L. terrestris and Isoptera with two general peaks for L. terrestris and a significant Isoptera peak under maize stover. Rainfall significantly influenced L. terrestris and Isoptera abundance, while within-season sampling time explained the observed fluctuations in Diplopoda, Holotrichia serrata, Araneae, Acrididae, and Formicidae. While Araneae was prevalent under maize stover, Elateridae, H. serrata and Araneae showed no distinct pattern in abundance. At low application rate, higher Shannon-Wiener diversity indices were apparent except for maize stover. Increasing application rate of the different organics amplified stimulation, abundance and persistence of macrofauna, and significantly increased diversity relative to the control. Application of N-based mineral fertiliser appeared to be detrimental to selective macrofauna (e.g., L. terrestris, Isoptera and Elateridae). Monte Carlo permutation test identified ammonium nitrate as the most influential and detrimental variable followed by organic resource quality, soil organic carbon (SOC) and application rate. Long-term co-application of organic and inorganic resources thus stimulated macrofaunal populations and maintained diversity. To sustain the productivity of the predominantly maize-based smallholder cropping systems, it is proposed that extension packages promote the inclusion of a minimum of at least 1.2 t carbon ha−1 annually towards improved soil health.