The Mt Cer Pluton, Serbia, is a complex laccolith-like intrusion (~ 60 km2), situated along the junction between the southern Pannonian Basin and northern Dinarides. It intrudes Palaeozoic metamorphic rocks causing weak to strong thermal effects. Based on modal and chemical compositions, four rock-types can be distinguished: (1) metaluminous I-type quartz monzonite/quartz monzodiorite (QMZD); (2) peraluminous S-type two-mica granite (TMG), which intrudes QMZD; (3) Stražanica granodiorite/quartz monzonite (GDS); and (4) isolated mafic enclaves (ME), found only in QMZD. 40K–39Ar dating and geological constraints indicate that the main quartz monzonite/quartz monzodiorite body of Mt Cer was emplaced not later than 21 Ma, whereas the emplacement ages of the Stražanica granodiorite/quartz monzonite and two-mica granites are estimated at around 18 and 16 Ma, respectively. The Mt Cer pluton is similar to the Mt Bukulja pluton, some 80 km southwestwards. Genesis of QMZD cannot be interpreted by fractional crystallization coupled with mixing or assimilation. It is best explained by a convection–diffusion process between mantle-derived minette/leucominette magmas and GDS-like magmas followed by two end-member magma mixing. The composition of GDS rocks suggests that GDS-like magmas could have formed by melting of lower crustal lithologies similar to amphibolite/metabasalts. The geochemistry of TMG is reproduced by an Assimilation/Fractional Crystallization model with a ratio of rate of assimilation to rate of fractional crystallization of 0.4, using the compositions of the least evolved TMG of the Bukulja pluton and adjacent metamorphic rocks as proxies for the parental magma and contaminant, respectively. The origin and evolution of the Mt Cer and adjacent Mt Bukulja plutons provide new constraints on the Tertiary geodynamics of the northern Dinarides–southern Pannonian region. The quartz monzonite/quartz monzodiorite is interpreted as a result of the Oligocene post-collisional Dinaride orogen-collapse, which included a limited lithosphere delamination, small-scale mantle upwelling, and melting of the lower crust. By contrast, the two-mica granite magmas formed through melting in shallower crustal levels during the extensional collapse in the Pannonian area.