PurposeTo develop a free‐running 3D radial whole‐heart multiecho gradient echo (ME‐GRE) framework for cardiac‐ and respiratory‐motion‐resolved fat fraction (FF) quantification.Methods(NTE = 8) readouts optimized for water–fat separation and quantification were integrated within a continuous non‐electrocardiogram‐triggered free‐breathing 3D radial GRE acquisition. Motion resolution was achieved with pilot tone (PT) navigation, and the extracted cardiac and respiratory signals were compared to those obtained with self‐gating (SG). After extra‐dimensional golden‐angle radial sparse parallel‐based image reconstruction, FF, R2*, and B0 maps, as well as fat and water images were generated with a maximum‐likelihood fitting algorithm. The framework was tested in a fat–water phantom and in 10 healthy volunteers at 1.5 T using NTE = 4 and NTE = 8 echoes. The separated images and maps were compared with a standard free‐breathing electrocardiogram (ECG)‐triggered acquisition.ResultsThe method was validated in vivo, and physiological motion was resolved over all collected echoes. Across volunteers, PT provided respiratory and cardiac signals in agreement (r = 0.91 and r = 0.72) with SG of the first echo, and a higher correlation to the ECG (0.1% of missed triggers for PT vs. 5.9% for SG). The framework enabled pericardial fat imaging and quantification throughout the cardiac cycle, revealing a decrease in FF at end‐systole by 11.4% ± 3.1% across volunteers (p < 0.0001). Motion‐resolved end‐diastolic 3D FF maps showed good correlation with ECG‐triggered measurements (FF bias of −1.06%). A significant difference in free‐running FF measured with NTE = 4 and NTE = 8 was found (p < 0.0001 in sub‐cutaneous fat and p < 0.01 in pericardial fat).ConclusionFree‐running fat fraction mapping was validated at 1.5 T, enabling ME‐GRE‐based fat quantification with NTE = 8 echoes in 6:15 min.