The Atlantic Forest fragments have suffered from the impacts of climate change, resulting in the increased production of Coarse Woody Debris (CWD), which needs to be evaluated in space and time to generate accurate estimates of carbon accumulation. Thus, the goals of this study were: i) to quantify the CWD volume, necromass, carbon stock and annual increment of carbon (AI<sub>carb</sub>) over a period of 4 years; and ii) to select the optimal combination of climatic, topographic, edaphic and intrinsic forest variables to accurately predict AI<sub>carb</sub>, using machine learning and multivariate analysis. The CWD volume, necromass and carbon stock increased between 2017 and 2020. The AI<sub>carb</sub> was 1.09 MgC.ha<sup>−1</sup>.year<sup>−1</sup> (2017–2018), 1.24 MgC.ha<sup>−1</sup>.year<sup>−1</sup> (2018–2019) and 2.31 MgC.ha<sup>−1</sup>.year<sup>−1</sup> (2019–2020). Statistical analysis indicated that climate variables had greater weight in the CWD carbon increment in the 2018–2019 and 2019–2020 periods, while edaphic, topographical and intrinsic forest variables were more important for the 2017–2018 period. Our findings showed that the carbon increase in CWD was linked to temporal and spatial variables within forests. These results demonstrate the importance of this parameter in the carbon cycle of forest ecosystems and highlight that there should be greater international research efforts to quantify this carbon pool.