Conventional agricultural practices such as intensive tillage and monoculture have accelerated soil degradation and reduced fertility in South Africa’s grain-producing regions, thereby constraining crop yields. Conservation agriculture (CA), which integrates reduced tillage, crop rotation, and cover cropping, is promoted to restore soil fertility by improving nutrient cycling. However, the mechanisms through which CA influences soil nutrient dynamics in semi-arid environments remain poorly understood. This study evaluated short-term nutrient responses to CA after three years of implementation at the Kenilworth Experimental Farm, Bloemfontein, South Africa. A randomised split-plot design was established with tillage (conventional vs. no-till) as main plots and cropping systems (maize monoculture, fallow–cereal rotation, maize–cover crop rotation, and legume–cover crop rotation) as subplots, replicated three times. Composite soil samples (0–30 cm) were collected at crop maturity and analyzed for phosphorus (P), copper (Cu), and manganese (Mn). Significant interactions between tillage and cropping systems were observed. No-till combined with a wheat–fallow rotation decreased Mn content by 24% compared to conventional tillage and wheat–fallow–maize systems, due to declines in effective cation exchange capacity. Compared to conventional tillage and maize monoculture systems, no-till maize monoculture increased Cu content by 22%, associated with elevated soil pH. Compared with maize monoculture, the maize–cover crop system decreased available P by 27%, likely due to P immobilisation in cover crop biomass. Overall, the results demonstrate that short-term adoption of CA in semi-arid regions generates divergent nutrient responses: some practices enhance micronutrient availability, while others constrain macronutrient supply. These findings highlight the complexity of nutrient cycling under CA and emphasise the need for system-specific nutrient management. The study provides mechanistic insights to refine CA practices for sustaining soil fertility and crop productivity in semi-arid South Africa.