Introducing artificial intelligence techniques in agriculture offers new opportunities for improving crop management, such as in coffee plantations, which constitute a complex agroforestry environment. This paper presents a comparative study of three deep learning frameworks: Deep Forest, RT-DETR, and Yolov9, customized for coffee plant detection and trained from images with a high spatial resolution (cm/pix). Each frame had dimensions of 640 × 640 pixels acquired from passive RGB sensors onboard a UAS (Unmanned Aerial Systems) system. The image set was structured and consolidated from UAS-RGB imagery acquisition in six locations along the Central Valley, Costa Rica, through automated photogrammetric missions. It was evidenced that the RT-DETR and Yolov9 frameworks allowed adequate generalization and detection with mAP50 values higher than 90% and mAP5095 higher than 54%, in scenarios of application with data augmentation techniques. Deep Forest also achieved good metrics, but noticeably lower when compared to the other frameworks. RT-DETR and Yolov9 were able to generalize and detect coffee plants in unseen scenarios that include complex forest structures within tropical agroforestry Systems (AFS).