<p>Integrating unoccupied aerial systems (UAS) into agricultural remote sensing has revolutionized several domains, including crop yield estimation. This research arises from the need to combat citrus greening disease, a major threat to citrus production. Accurately estimating crop yields is crucial for evaluating the effectiveness of treatments and controls for this disease. In response, our study examined the efficacy of phenotypic data extracted from multi-temporal RGB and multispectral UAS images in estimating individual citrus tree yields before harvest and then using this as an indicator to analyze the effectiveness of the treatments and control choice.</p> <p>This study presents machine learning-based regression models for estimating individual citrus tree yields, utilizing the diverse features extracted to provide comprehensive insights into the citrus trees under investigation. Four machine learning algorithms, random forest regression, extreme gradient boosting regression, adaptive boosting, and support vector regression, were employed to build the yield estimation models. The experiment was designed in two phases: single-temporal and multi-temporal modeling.</p>