We combined micro computer tomography with Fe and Si isotope measurements of Mokoia, Allende and Grosnaja chondrules. Ten Mokoia chondrules contain 0.9 to 11.8 vol.% opaque phases (metal + sulfide), and 6 Allende chondrules contain 0.0 to 6.6 vol.% opaque phases. Hence, the Fe isotope composition of many chondrules is dominated by the Fe isotope composition of their opaque phases. We studied Fe isotopes of 35 bulk chondrules. The range is different for each of the three meteorites studied and largest for Allende with δ56Fe ranging from − 0.82 to + 0.37‰. Six out of seven chondrules analysed for their Si isotope composition in Mokoia and Grosnaja have similar δ29Si of around − 0.12‰. One anomalous chondrule in Mokoia has a δ29Si of + 0.58‰. We exclude isotopically heterogeneous chondrule precursors and different isotopic chondrule reservoirs as the source of the observed Fe isotope variation among bulk chondrules. We conclude that the observed bulk chondrule Fe isotope variation is the result of evaporation and re-condensation processes in a nebula setting with high dust densities, required to explain the comparatively low isotope fractionations. Subsequent parent body alteration slightly overprinted this pre-accretionary Fe isotope variation.