Soybean is an essential crop to fight global food insecurity and is of great economic importance around the world. Along with genetic improvements aimed at boosting yield, soybean seed composition also changed. Since conditions during crop growth and development influences nutrient accumulation in soybean seeds, remote sensing offers a unique opportunity to estimate seed traits from the standing crops. Capturing phenological developments that influence seed composition requires frequent satellite observations at higher spatial and spectral resolutions. This study introduces a novel spectral fusion technique called multiheaded kernel-based spectral fusion (MKSF) that combines the higher spatial resolution of PlanetScope (PS) and spectral bands from Sentinel 2 (S2) satellites. The study also focuses on using the additional spectral bands and different statistical machine learning models to estimate seed traits, e.g., protein, oil, sucrose, starch, ash, fiber, and yield. The MKSF was trained using PS and S2 image pairs from different growth stages and predicted the potential VNIR1 (705 nm), VNIR2 (740 nm), VNIR3 (783 nm), SWIR1 (1610 nm), and SWIR2 (2190 nm) bands from the PS images. Our results indicate that VNIR3 prediction performance was the highest followed by VNIR2, VNIR1, SWIR1, and SWIR2. Among the seed traits, sucrose yielded the highest predictive performance with RFR model. Finally, the feature importance analysis revealed the importance of MKSF-generated vegetation indices from fused images.