Crop monitoring and appropriate agricultural management practices of elite germplasm will enhance bioenergy’s efficiency. Unmanned aerial systems (UAS) may be a useful tool for this purpose. The objective of this study was to assess the use of UAS with true color and multispectral imagery to predict the yield and total cellulosic content (TCC) of newly created energy cane germplasm. A trial was established in the growing season of 2016 at the Texas A&M AgriLife Research Center in Weslaco, Texas, where 15 energy cane elite lines and three checks were grown on experimental plots, arranged in a complete block design and replicated four times. Four flights were executed at different growth stages in 2018, at the first ratoon crop, using two multi-rotor UAS: the DJI Phantom 4 Pro equipped with RGB camera and the DJI Matrice 100, equipped with multispectral sensor (SlantRange 3p). Canopy cover, canopy height, NDVI (Normalized Difference Vegetation Index), and ExG (Excess Green Index) were extracted from the images and used to perform a stepwise regression to obtain the yield and TCC models. The results showed a good agreement between the predicted and the measured yields (R2 = 0.88); however, a low coefficient of determination was found between the predicted and the observed TCC (R2 = 0.30). This study demonstrated the potential application of UAS to estimate energy cane yield with high accuracy, enabling plant breeders to phenotype larger populations and make selections with higher confidence.