Accurately estimating crop performance under various fertilizer levels in a rapid and non-destructive manner has become a vital aspect of precision agriculture technology for both economic and environmental benefits. This study aimed to estimate different sugar beet parameters, such as total chlorophyll (Chlt), chlorophyll a (Chla), chlorophyll b (Chlb), root yield (RY), sugar yield (SY), and sugar content (SC) under five nitrogen (N) levels (0, 30, 60, 90, and 120 kg N ha−1). This was achieved by using a combination of the gradient boosting regression (GBR) model with published and newly developed two- and three-band spectral indices (2D- and 3D-SRIs). The results showed that the N levels had the highest proportion of variations (80.4–92.9%) for all parameters, except for SC, which had more variation (59.9%) according to year than the N levels (37.2%). All parameters, except SC, showed a significant increase with gradually increasing N levels. Additionally, the N levels displayed linear and strong positive relationships with the chlorophyll parameters, and linear and strong negative relationships with SC, while these relationships were quadratic and strong with RY and SY. Several published and novel 3D-SRIs exhibited moderate to strong relationships (R2 = 0.65–0.89) with all parameters. The newly developed 3D-SRIs, which involve wavelengths from the visible, near-infrared, and red-edge regions, such as NDI536, 538, 534, NDI738, 750, 542, and NDI448, 734, 398, were effective in accurately estimating all parameters. Combining 2D-SRIs, 3D-SRIs, and the aggregate of all spectral indices (ASRIs) with GBR models could be a robust strategy for estimating the six observed parameters with reasonable precision. The GBR-ASF-6 SRIs and the GBR-ASF-7 SRIs models performed better in predicting Chl content and SC with R2 values of 0.99 and 0.99 (RMSE = 0.073 and 1.568) for the training dataset and R2 values of 0.65 and 0.78 (RMSE = 0.354 and 6.294) for the testing datasets, respectively. The obtained results concluded that published and newly developed 3D-SRIs, GBR based on 2D-SRIs or 3D-SRIs, and the aggregate of all ASRIs can be used in practice to accurately estimate the Chl content, production, and quality of sugar beet across a wide range of N levels under semiarid conditions.