Prediction of carbon dioxide (CO2) emissions from agricultural soil is vital for efficient and strategic mitigating practices and achieving climate smart agriculture. This study aimed to evaluate the ability of two machine learning algorithms [gradient boosting regression (GBR), support vector regression (SVR)], and two deep learning algorithms [feedforward neural network (FNN) and convolutional neural network (CNN)] in predicting CO2 emissions from Maize fields in two agroclimatic regions i.e., continental (Debrecen-Hungary), and semi-arid (Karaj-Iran). This research developed three scenarios for predicting CO2. Each scenario is developed by a combination between input variables [i.e., soil temperature (Δ), soil moisture (θ), date of measurement (SD), soil management (SM)] [i.e., SC1: (SM + Δ + θ), SC2: (SM + Δ), SC3: (SM + θ)]. Results showed that the average CO2 emission from Debrecen was 138.78 ± 72.04 ppm (n = 36), while the average from Karaj was 478.98 ± 174.22 ppm (n = 36). Performance evaluation results of train set revealed that high prediction accuracy is achieved by GBR in SC1 with the highest R² = 0.8778, and lowest root mean squared error (RMSE) = 72.05, followed by GBR in SC3. Overall, the performance MDLM is ranked as GBR > FNN > CNN > SVR. In testing phase, the highest prediction accuracy was achieved by FNN in SC1 with R² = 0.918, and RMSE = 67.75, followed by FNN in SC3, and GBR in SC1 (R² = 0.887, RMSE = 79.881). The performance of MDLM ranked as FNN > GRB > CNN > SVR. The findings of the research provide insights into agricultural management strategies, enabling stakeholders to work towards a more sustainable and climate-resilient future in agriculture.