Goethite (α-FeOOH) is dispersed throughout the earth's surface, and its propensity to recrystallize in aqueous solutions determines whether this mineral is a source or sink for critical trace elements in the environment. Under reducing conditions, goethite commonly coexists with aqueous Fe(II) (Fe(II)aq), which accelerates recrystallization by coupled electron transfer and atom exchange. Quantifying the amount of the mineral phase that exchanges its structural Fe(III) atoms with Fe(II)aq is complicated by recrystallization models with untested assumptions of whether, and to what extent, the recrystallized portion of the mineral continues to interact with the solution. Here, we reacted nanoparticulate goethite with 57Fe-enriched Fe(II)aq and used atom probe tomography (APT) to resolve the three-dimensional distribution of Fe isotopes in goethite at the sub nm scale. We found that the 57Fe tracer isotope is enriched in the bulk structure (tens of nanometers deep), with some samples having 57Fe penetration throughout at a level that is similar to the isotopic composition of Fe(II)aq. This suggests that some particles undergo near-complete recrystallization. In other cases, however, the distribution of 57Fe is more heterogeneous and generally concentrates near the particle periphery. Nanoparticle encapsulation and subsequent APT can hence capture hidden recrystallization mechanisms which are critical to predicting mineral reactivity in aqueous solutions.