We present the results of Nd and Pb isotope studies of late Neoproterozoic–early Paleozoic granitoids of the Kaa-Khem batholith, which formed in different geodynamic settings within the early Caledonian structures of Eastern Tuva (Altai–Sayan sialic area). Based on the obtained isotope data, we assess the role of different source materials in the formation of melts for these granitoids and compare these rocks with coeval granitoids from the Lake Zone of Mongolia. The plagiogranitoid associations of the island arc stage of the Kaa-Khem batholith formation (572–562 Ma) are characterized by mantle Nd isotope values. In contrast, the Pb isotope characteristics of these intrusive associations correspond to an upper-crust source formed predominantly by terrigenous sediments. The granitoid associations of the accretion–collision stage of the Kaa-Khem batholith formation (512–450 Ma) have a less radiogenic primary Pb isotope composition as compared with the island arc granitoids. Evidently, during the magma formation at this stage, the relative role of terrigenous material decreased, while the role of depleted mantle material increased. At the same time, the decrease in ɛNd values in the granitoids as compared with the depleted mantle indicates that, along with the upper-mantle component, the role of the lower-crust component increased. These Nd and Pb isotope characteristics of the accretionary granitoids of the Kaa-Khem batholith indicate a significant contribution of the lower-crust source to their formation. This source is the crystalline basement of the Tuva–Mongolian microcontinent. The Pb isotope characteristics of the accretion–collision granitoids of the Kaa-Khem batholith are shifted to the upper-crust compositions relative to those of the Lake Zone granitoids. The reason is that the latter formed predominantly through the transformation of early Caledonian island arc complexes, which were generated with a higher portion of mantle component.