No consensus currently exists about how climate change should affect the status of soil organic matter (SOM) in the tropics. In this study, we analyse the impact of climate change on the underlying mechanisms controlling SOM dynamics in a ferralsol under two contrasting tropical crops: maize (C4 plant) and banana (C3 plant). We model the effect of microbial thermal adaptation on carbon (C) mineralisation at the crop system scale and introduce it in the model STICS, which was previously calibrated for the soil-crop systems tested in this study. Microbial thermal adaptation modelling is based on a reported theory for thermal acclimation of plant and soil respiration. The climate is simulated from 1950 to 2099 for the tropical humid conditions of Guadeloupe (French Antilles), using the ARPEGE model and the IPCC emission scenario A1B. The model predicts increases of 3.4 °C for air temperature and 1100 mm yr−1 for rainfall as a response to an increase of 375 ppm for atmospheric carbon dioxide concentration in the 2090–2099 decade compared with the 1950–1959 decade. The results of the STICS model indicate that the crop affects the response of SOM to climate change by controlling the change in several variables involved in C dynamics: C input, soil temperature and soil moisture. SOM content varies little until 2020, and then it decreases faster for maize than for banana. The decrease is weakened under the hypothesis of thermal adaptation, and this effect is greater for maize (−180 kg C ha−1 yr−1 without adaptation and −140 kg C ha−1 yr−1 with adaptation) than for banana (−60 kg C ha−1 yr−1 and −40 kg C ha−1 yr−1, respectively). The greater SOM loss in maize is mainly due to the negative effect of warming on maize growth decreasing C input from residues. Climate change has a small effect on banana growth, and SOM loss is linked to its effect on C mineralisation. For both crops, annual C mineralisation increases until 2040, and then it decreases continuously. Thermal adaptation reduces the initial increase in mineralisation, but its effect is lower on the final decrease, which is mainly controlled by substrate limitation. No stabilisation in SOM status is attained at the end of the analysed period because C mineralisation is always greater than C input. Model predictions indicate that microbial thermal adaptation modifies, but does not fundamentally change the temporal pattern of SOM dynamics. The vegetation type (C3 or C4) plays a major role in SOM dynamics in this tropical soil because of the different impact of climate change on crop growth and then on C inputs