Magnesium (Mg) and zinc (Zn) isotopes have been applied to trace whether surface carbonates have been recycled into the deep mantle beneath Balkan Peninsula, where a stagnant slab exists in the mantle transition zone. Here we investigate a suite of Cenozoic sodic alkaline basaltic rocks (Na2O/K2O > 1), called the East Serbian Mafic Alkaline Rocks (ESMAR) from East Serbia in central Balkan Peninsula, which is an important segment of the Tethyan orogenic belt. The ESMAR have lower δ26MgDSM-3 (−0.49‰ to −0.39‰; n = 21) and higher δ66ZnJMC 3-0749L (0.35‰ to 0.45‰; n = 21) than those of normal mantle-derived melts (e.g., mid-oceanic ridge basalts; MORBs; δ26Mg = −0.25 ± 0.06‰ and δ66Zn = 0.27 ± 0.06‰). After excluding the effects of low-T and magmatic processes, the Mg and Zn isotopic anomalies of the ESMAR are proposed to have been caused by recycled carbonates in their mantle sources. The significantly low Zn contents, Zn/Fe and Fe/Mn ratios of the ESMAR indicate a highly depleted peridotitic mantle source. Their major element compositions (e.g., low Ti2O and high CaO/Al2O3) are consistent with those of experimental partial melts of “peridotite + CO2”. The incremental batch melting and end-member mixing models suggest that ∼5–10% of Mg-rich carbonates (dolomite and magnesite) have been recycled into the mantle sources of the ESMAR. Our results provide evidence for deep recycling of carbonates related to subduction of a Tethyan oceanic slab, most likely into the mantle transition zone beneath the Balkan Peninsula. This contributes a significant part of global deep carbon cycling during the Cenozoic.