Intensity inhomogeneity is a great challenge for automated organ segmentation in magnetic resonance (MR) images. Many segmentation methods fail to deliver satisfactory results when the images are corrupted by a bias field. Although inhomogeneity correction methods exist, they often fail to remove the bias field completely in knee MR images. We present a new iterative approach that simultaneously predicts the segmentation mask of knee structures using a 3D U-net and estimates the bias field in 3D MR knee images using partial convolution operations. First, the test images run through a trained 3D U-net to generate a preliminary segmentation result, which is then fed to the partial convolution filter to create a preliminary estimation of the bias field using the segmented bone mask. Finally, the estimated bias field is then used to produce bias field corrected images as the new inputs to the 3D U-net. Through this loop, the segmentation results and bias field correction are iteratively improved. The proposed method was evaluated on 20 proton-density (PD)-weighted knee MRI scans with manually created segmentation ground truth using 10 fold cross-validation. In our preliminary experiments, the proposed methods outperformed conventional inhomogeneity-correction-plus-segmentation setup in terms of both segmentation accuracy and speed.