Chemical shift-encoded (CSE)-MRI enables accurate and precise quantification of proton density fat-fraction (PDFF) in the liver. Widely used 3D multi-echo spoiled gradient echo (SGRE) CSE-MRI requires reliable breath-holding to avoid motion-related artifacts. This is a major limitation for children, the elderly, and sick patients. Free-breathing 2D sequential CSE-MRI is motion-robust, however, suffers from low signal-to-noise-ratio (SNR). To overcome these limitations, we combined variable flip angle (VFA) 2D acquisitions and nonlocal means (NLM) motion-corrected averaging. In this prospective study, free-breathing multi-repetition VFA-NLM demonstrated high SNR and reduced artifacts compared to the conventional 3D-SGRE, while preserving accuracy of PDFF quantification.