Numerous Cretaceous metamorphic core complexes (MCCs) extend from Transbaikalia in Russia to northern Mongolia within the Central Asian Orogenic Belt. We investigated the Buteel and Zagan MCCs in detail. Shear sense indicators in mylonitized rocks show footwall-to-the-NW tectonic transport. Single zircon dating of footwall rocks in the Buteel MCC establishes the emplacement of granitoid orthogneiss precursors at 240–211 Ma, a felsic metavolcanic rock at 265.0 ± 1.2 Ma, a syenite at 265.5 ± 1.2 Ma and a metarhyolite of the pre-granitoid basement at 553.6 ± 2.9 Ma. A peralkaline granite intruding orthogneisses of the Zagan MCC has a new U–Pb zircon age of 151.6 ± 0.7 Ma. 40Ar/39Ar ages of 133.5 ± 1.8 Ma of hornblende from amphibolite and 122.6 ± 1.8 Ma of biotite from mylonitized gabbro–dolerite of the Buteel MCC are interpreted as cooling ages representing the time of deformation in the footwall. Geological data suggest that the MCCs in Transbaikalia and northern Mongolia formed as a result of extension in a crust that had previously been thickened by abundant calc-alkaline magmatism in an Andean-type setting on the border of the closing Mongol–Okhotsk ocean, by widespread collisional to post-collisional thrusting, and by extensive alkaline–peralkaline magmatism.