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Ensuring food security in precision agriculture requires early prediction of soybean yield at various scales within the United States (U.S.), ranging from international to local levels. Accurate yield estimation is essential in preventing famine by providing insights into food availability during the growth season. Numerous deep learning (DL) algorithms have been developed to estimate soybean yield effectively using time-series remote sensing (RS) data to achieve this goal. However, the training data with short time spans can limit their ability to adapt to the dynamic and nuanced temporal changes in crop conditions. To address this challenge, we designed a 3D-ResNet-BiLSTM model to efficiently predict soybean yield at the county level across the U.S., even when using training data with shorter periods. We leveraged detailed Sentinel-2 imagery and Sentinel-1 SAR images to extract spectral bands, key vegetation indices (VIs), and VV and VH polarizations. Additionally, Daymet data was incorporated via Google Earth Engine (GEE) to enhance the model's input features. To process these inputs effectively, a dedicated 3D-ResNet architecture was designed to extract high-level features. These enriched features were then fed into a BiLSTM layer, enabling accurate prediction of soybean yield. To evaluate the efficacy of our model, its performance was compared with that of well-known models, including the Linear Regression (LR), Random Forest (RF), and 1D/2D/3D-ResNet models, as well as a 2D-CNN-LSTM model. The data from a short period (2019 to 2020) were used to train all models, while their accuracy was assessed using data from the year 2021. The experimental results showed that the proposed 3D-Resnet-BiLSTM model had a superior performance compared to the other models, achieving remarkable metrics (R2 = 0.791, RMSE = 5.56 Bu Ac−1, MAE = 4.35 Bu Ac−1, MAPE = 9%, and RRMSE = 10.49%). Furthermore, the 3D-ResNet-BiLSTM model showed a 7% higher R2 than the ResNet and RF models and an enhancement of 27% and 17% against the LR and 2D-CNN-LSTM models, respectively. The results highlighted our model's potential for accurate soybean yield predictions, supporting sustainable agriculture and food security. [ABSTRACT FROM AUTHOR]