This study documents the chemical and textural responses of zircon in the Elba igneous complex, with particular reference to the 7- to 7.8-Ma-old Monte Capanne pluton in relation to its coeval volcanic counterpart (Capraia), using BSE imaging and quantitative electron microprobe analyses. The Monte Capanne pluton displays multiple field and geochemical evidence for magma mixing. The samples we have investigated (including monzogranitic, mafic enclave and dyke samples) display similar zircon textures and are associated with an extremely large range of trace and minor element (Hf, Y, HREE, Th, U) compositions, which contrast with relatively simple textures and zoning patterns in zircons from a Capraia dacite. We have used a relatively simple textural classification (patchy zoning, homogenous cores, oscillatory zoning and unzoned zircon) as the basis for discussing the chemical composition and chemical variation within zircons from the Monte Capanne pluton. Based on these data and other works (Dini et al. 2004 in Lithos 78:101–118, 2004) , it is inferred that mixing between metaluminous and peraluminous melts occurred early in the evolution of the Monte Capanne magma chamber. In particular, mixing was responsible for the development of the patchy-zoning texture in the zircon cores, which was associated with reactions between other accessory phases (including monazite, apatite, allanite), which we infer to have significantly affected the Th distribution in zircon. Zircons from the MC pluton displaying “homogeneous cores” have chemical affinities with zircons in the coeval Capraia volcanic system, consistent with the participation of a Capraia-like mantle end-member during mixing. Further zircon growth in the MC pluton produced the oscillatory zoning texture, which records both long-term (crystal fractionation) and transient (recharge with both silicic and mafic magmas) events in a hybrid magma chamber. It is inferred that Hf and the Th/U ratio cannot be used alone to infer magmatic processes due to their dependency on temperature, nor are they a diagnostic feature of xenocrystic grains. This study shows that zircon chemistry coupled with detailed textural analysis can provide a powerful tool to elucidate the complex evolution of a magma system.