Cocoa (Theobroma cacao) farmers in Sulawesi, Indonesia typically use subsidised, ammonium-based rice fertilisers that in combination with poor agricultural practices have resulted in soil acidification, loss of organic matter, aluminium toxicity and lower soil fertility. As a result, these soils are only marginally appropriate for replanting cocoa to boost production. A field experiment was performed to test alternative soil amendments for successful replanting of cocoa on these deficient soils. In a trial with a randomised block design, 6-month old seedlings, top-grafted with the local MCC02 clone, were planted under light Gliricidia sepium shade and after 3 months treated quarterly with two options of mineral fertilisers: either a customised fertiliser, consisting of Nitrabor (a combination of calcium nitrate and boron), dolomite, rock phosphate and KCl or a NPK/urea mix used by farmers, each supplied with or without ‘micronutrient’ rock salt, organic fertiliser and beneficial microorganisms or their culture medium, a mixture of chitin and amino acids (a total of 20 treatments). Over a 4-year period, the marginal mean rates of stem diameter increment and flowering score were higher in customised fertiliser than NPK/urea treatments. The average growth rate was highest in the first year and was increased by supplying organic fertiliser. A significant correlation (r = 0.22, p < 0.05) occurred between growth and available P, but concentrations of available P were higher in the NPK/urea plots, which also had lower mean growth rates. Combined supply of organic fertiliser and microbes increased available P, as well as growth rates, in both the customised and NPK/urea treatments. In contrast, NPK/urea-treated plots without these amendments demonstrated very low growth rates. The customised formulation was more effective with or without added organic fertiliser or inoculated microbes. Micronutrient supply stimulated flowering. Growth rates in trees supplied with NPK/urea were also promoted by micronutrients. Leaf flush production occurred in regular cycles and was unaffected by the nutrient amendments. After 3 years, the customised and organic fertiliser application increased soil pH and exchangeable Ca and Mg concentrations, although they remained below recommended levels for cocoa production. These treatments had little impact on soil C content (about 1.3%) which was also deficient. Exchangeable Al and total Zn concentrations were higher in soils amended with NPK/urea. The results of the trial provide evidence that utilisation of organic fertiliser in combination with customised nitrate-based formulations improves cocoa establishment, growth and soil properties and should be recommended as a replacement for the NPK/urea fertilisers traditionally used by farmers.