Low soil fertility, high rates of fertilizer application and low yields and quality are major problems in intensive banana production in acid soils of south China. A field experiment was carried out for two years to determine the optimum management practices for maximizing soil health and banana yield and quality. The experiment consisted of an unamended control (CK) and lime (Lime), calcium magnesium phosphate fertilizer (CMP), organic fertilizer (OF), and organic fertilizer combined with calcium magnesium phosphate fertilizer (OFC) treatments. Soil nutrient concentrations and banana shoot biomass, nutrient uptake, yield and fruit quality were determined. Application of lime and CMP was found to increase soil pH and nutrient availability and increase banana yield. Yet, the banana biomass and yields in the Lime and CMP treatments were significantly lower than those in the OF and OFC treatments in which soil organic matter (SOM) content increased. Total soluble solids and soluble sugar contents increased in the CMP and organic fertilizer treatments. A consistent increase in Mg concentrations in banana leaves over the two years in the CMP and organic fertilizer treatments indicates that Mg is essential for banana production and quality. Short-term adding Mg from banana corms increased total soluble solids and soluble sugar content. The application of organic fertilizer combined with CMP or Mg solution is therefore recommended to increase soil health and promote the yield and quality of banana in intensively managed plantations in subtropical regions.