Soil health and fertility are indexed by soil organic carbon (SOC) content. Soil management through good agricultural practices that enhance and sustain SOC is vital for soil fertility. We examined the influence of soil fertility management strategies on SOC concentrations in different particle size fractions under a maize cropping system. We laid the experiment in a randomized complete block design, with 14 treatments replicated 4 times, and used the following inputs: inorganic fertilizer (Mf), maize residue +inorganic fertilizer (RMf), maize residue + inorganic fertilizer, and goat manure (RMfM), maize residue + goat manure + Dolichos Lablab L intercrop (RML), maize residue + Tithonia diversifolia + goat manure (RTiM) and maize residue + Tithonia diversifolia + phosphate rock (Minjingu) (RTiP) and a Control (no inputs) under reduced tillage (Mt) or conventional tillage (Ct). Soil samples were collected from two depths, 0–5 cm, and 5–15 cm. We determined the content of organic carbon in three physical fractionation: coarse fractions (1.7 mm, 500 µm sieve), medium fractions (250 µm and 90 µm), and a fine fraction (75 µm). Results showed that treatment with maize residues, goat manure, and legume intercrop (MtRML and CtRML) resulted in higher SOC in most fractions, irrespective of the soil depth. The SOC concentration significantly (p < 0.0001) differed across treatments and depth. It was followed by maize residue, goat manure, and inorganic fertilizer treatments, and the least was inorganic fertilizer treatment. This underpins the importance of manure application and crop residue retention in increasing SOC amounts. Reduced tillage did not influence the SOC amounts during the sampling period in the experimentation site. This study highlights the possibility of improving agricultural productivity by improving soil fertility through a combination of different agricultural soil fertility amendments in Sub-Saharan Africa.