Export agriculture in the Caribbean is often blamed for pollution of soils and water resources. At the same time, the reduction of preferences in the international markets for major agricultural exports from the Caribbean induced a partial reorientation of the agriculture towards the local markets, which included crop diversification. This study was carried out to assess the sustainability of that agricultural switch with respect to maintaining, increasing or decreasing soil organic carbon (SOC) stocks. We analysed the impact of export crops (sugarcane and banana monocultures) and diversified agriculture (as monoculture or in rotation with export crops) on SOC stocks using the case study of Guadeloupe (Lesser Antilles). Agriculture in Guadeloupe involves a mosaic of soils, climates, crops and farming practices, which well represent the tropical conditions of export and diversified agriculture in the region. The study was based on: (i) a soil database including information on the SOC stocks of numerous cropping system—agro-ecological region (AER) situations, (ii) a survey of farming practices performed on a network of 382 farmers (e.g. crop rotations and yields, management of residues and organic amendments), and (iii) the development of a simple model of annual C inputs and outputs to assess SOC dynamics at the AER scale. The model was calibrated and evaluated using 253 plots and included 827 SOC measurements selected from the soil database. The model produced satisfactory estimates of changes in SOC stocks and provided an explanation for differences between cropping systems and AERs in terms of the C inputs and outputs. While sugarcane and banana monocultures were able to preserve or increase SOC, diversification was likely to reduce it. These differences were due to higher C inputs from crop residues together with lower C outputs for export agriculture. Lower SOC outputs by mineralization were mainly associated with the longer cycle of these pluriannual crops (5 yr), which decreased the impact of soil tillage at planting. Banana monoculture in the most humid AERs was the only cropping system that displayed a clear pattern of C sequestration (+0.5 Mg C ha−1 yr−1). The highest SOC losses were observed with vegetable crops in the same AERs (e.g. −2.0 Mg C ha−1 yr−1). Calculations made using the model indicated that the sustainability of diversified agriculture in the Caribbean might be reinforced by adopting reduced soil tillage, organic amendments and the liming of the more acid soils to increase yields and crop residues. The results of this study suggest that the implementation of new agricultural policies to reduce the negative environmental impacts of export crops should involve measures to preserve their positive effect on SOC storage.