In a false-time series, the temporal development of cocoa–gliricidia carbon (C) stocks and soil organic carbon (SOC) were investigated in Napu and Palolo Valleys of Central Sulawesi, Indonesia. As a first step, the Functional Branch Analysis (FBA) method was used to develop allometric equations for the above- and below-ground growth of cocoa and gliricidia. FBA resulted in shoot–root ratios of 2.54 and 2.05 for cocoa and gliricidia, respectively. In Napu and Palolo, the trunk diameter and carbon levels per gliricidia tree were always much greater than that of cocoa. The highest aerial carbon levels were attained at year four in Napu (aerial cocoa–gliricidia = 20,745.2 kg C ha−1) and at year five in Palolo (aerial cocoa–gliricidia = 38,857.0 kg C ha−1). After years four or five, however, the reduced stocking density of gliricidia attributed to a loss of aerial C. During the time spans in question, SOC remained fairly stable though slightly decreasing in Napu and slightly increasing in Palolo. The SOC harbored a vastly greater amount of system C (one-half and one-third of SOC in the 0–15 cm stratum in Napu and Palolo, respectively) relative to tree components. Eight years (Napu) or 15 years (Palolo) after conversion of a rainforest to cocoa–gliricidia agroforestry caused an 88% and 87% reduction of aerial C-stocks in Napu and Palolo, respectively.