In this paper, we report a spectroscopic study of natural type Ib-IaA diamonds containing Y centers subjected to high-pressure high-temperature treatment at 7–7.5 GPa and 1700–2200◦ C. Diamond samples showing the Y centers as the dominant absorption feature in the infrared spectra were selected from a collection of natural diamonds from alluvial placers of the northeastern Siberian Platform. The samples were investigated by spectroscopic techniques before and after each annealing stage. It was found that upon annealing at temperatures higher than 2000◦ C, the defect-induced one-phonon spectra changed from the Y centers to a new form with a characteristic band peaking at 1060 cm−1 . Photoluminescence spectra of the samples were modified after each annealing stage starting from 1700◦ C. The most significant changes in photoluminescence occurred at temperatures higher than 2000◦ C and were associated with a sharp increase of the intensity of an emission band peaking at about 690 nm. A comparison with natural red-luminescing diamonds from Yakutian kimberlite pipes was performed. It was concluded that the observed 1060 cm−1 IR band and the 690 nm red emission band are genetically related to the Y centers and that defects or impurities responsible for the Y centers appear quite widespread in natural diamonds from various deposits worldwide.