Zircon from two types of orthogneisses (inheritance-rich and inheritance-poor) from Sierra Nevada (Betic Cordillera, Spain) was investigated by integrating U–Pb geochronology, cathodoluminescence and back-scattered SEM imaging, laser-ablation inductively coupled plasma mass spectrometry analyses and Raman spectroscopy to examine the conditions of magmatic zircon growth and the variable extent and mechanisms of the Alpine modifications. Zircon from inheritance-rich gneiss consists of two main domains: inherited (Neoproterozoic-to-Early Paleozoic and Devonian) cores and magmatic overgrowths, which provided 206Pb/238U concordant ages of 286 ± 3 Ma. In inheritance-poor gneiss, zircons consist of magmatic cores and very altered rims defining a discordia with an upper intercept with the Concordia at 287 + 21 –22 Ma and a lower intercept at 20.8 + 48.6 –20.8 Ma. Magmatic domains of zircon from inheritance-rich gneiss have lower rare-earth element (REE) contents than magmatic domains from inheritance-poor gneiss, reflecting the less evolved nature of the melt. Altered domains in zircon from inheritance-poor gneiss show greater U concentrations, lower REE concentrations and lower Th/U ratios relative to the cores, interpreted as representing Pb loss from the U-rich magmatic domains during the Alpine event. Morphological changes within single grains and between populations reflects the evolution during magmatic cooling. We show that, whereas classic methods allow two different interpretations for the geodynamic setting of the two types of gneisses, a complete study of composition, morphology and structure of zircon can help to decide that a model based on a common source for the granitic melt better fits the zircon characteristics than a model based on melts generated in two different geotectonic settings.