Zircon and apatite grains from three types of variably contaminated quartz diorite were analyzed in the Gęsiniec Intrusion (SW Poland). The zircon isotopic compositions (εHf300 = − 5.5–0 and δ18O = 5.6–9.3‰) are consistent with contamination processes. Zircon is characterized by an increase in U, Th, Pb and REE from the least to the most evolved quartz diorite type. Apatite is characterized by ranges in trace element concentrations and, with the progress of contamination, its composition evolves from those typical for I-type granites toward those typical for S-type. Isotopic and trace element variations in zircon and apatite correlate with Sr isotopic composition of plagioclase (87Sr/86Sr300 = 0.7069–0.7084; Pietranik and Waight, 2008). However, both Sr isotopic composition of plagioclase and trace element composition of apatite could be homogenized by late-stage resorption, leaving zircon as the only record of contamination processes that predate resorption. Comparison between plagioclase and zircon isotopic composition is consistent with both plagioclase cores and zircons recording similar stages of magma contamination. Comparison between plagioclase and apatite composition indicates that crystallization of apatite was contemporaneous with crystallization of plagioclase rims. The preferred interpretation of isotopic and trace element variations observed in different grains is a two-stage contamination by crustally derived magmas. Early contamination was probably dominated by material typical of the lower crust, i.e. with none or only small amounts of a sedimentary component, as indicated by low δ18O in zircon (5.6–6.5‰) in both the least and the most contaminated types. Later contamination was dominated by crustally derived magmas containing more than 20% of a sedimentary component, as the most contaminated sample includes zircon with δ18O up to 9.3‰. Partial melts generated from an “S-type granite” source are the most probable contaminant for this second stage contamination, as indicated by apatite trace element composition. In general, isotopic and chemical composition of plagioclase, zircon and apatite provides complementary information on magmatic processes, but records a longer time span than a single mineral only due to their diachronous crystallization histories.