The European Commission introduces the Control by Monitoring through new technologies to manage Common Agricultural Policy funds through the Regulation 2018/746. The advances in remote sensing have been considered one of these new technologies, mainly since the European Space Agency designed the Copernicus Programme. The Sentinel-1 (radar range) and Sentinel-2 (optical range) satellites have been designed for monitoring agricultural problems based on the characteristics they provide. The data provided by the Sentinel 2 missions, together with the emergence of different scientific disciplines in artificial intelligence —especially machine learning— offer the perfect basis for identifying and classifying any crop and its phenological state. Our research is based on developing and evaluating a pixel-based supervised classification scheme to produce accurate rice crop mapping in a smallholder agricultural zone in Calasparra, Murcia, Spain. Several models are considered to obtain the most suitable model for each element of the time series used; pixel-based classification is performed and finished with a statistical treatment. The highly accurate results obtained, especially across the most significant vegetative development dates, indicate the benefits of using Sentinel-2 data combined with Machine Learning techniques to identify rice crops. It should be noted that it was possible to locate rice crop areas with an overall accuracy of 94% and standard deviation of 1%, which could be increased to 96% (±1%) if we focus on the months of the crop’s highest development state. Thanks to the proposed methodology, the on-site inspections carried out, 5% of the files, have been replaced by remote sensing evaluations of 100% of the analyzed season files. Besides, by adjusting the model input data, it is possible to detect unproductive or abandoned plots.