In situ techniques with high temporal, spatial and chemical resolution are key to understand ubiquitous solid-state phase transformations, which are crucial to many technological applications. Hard X-ray spectro-imaging can visualize electrochemically driven phase transformations but demands considerably large samples with strong absorption signal so far. Here we show a conceptually new data analysis method to enable operando visualization of mechanistically relevant weakly absorbing samples at the nanoscale and study electrochemical reaction dynamics of iron fluoride, a promising high-capacity conversion cathode material. In two specially designed samples with distinctive microstructure and porosity, we observe homogeneous phase transformations during both discharge and charge, faster and more complete Li-storage occurring in porous polycrystalline iron fluoride, and further, incomplete charge reaction following a pathway different from conventional belief. These mechanistic insights provide guidelines for designing better conversion cathode materials to realize the promise of high-capacity lithium-ion batteries.