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Yellow color in gem corundum is commonly caused by Fe3+ impurity replacing Al3+ in the Al2O3 structure. For two decades beryllium-assisted heat treatment has been introduced to produce yellow sapphires from colorless, green, or light blue sapphires. The roles of beryllium atoms in corundum structure have been proposed in different ways either triggering structural defects or being as catalysts. Thus, the research experiments were conducted to evaluate these contradictions by applying the UV–vis excitation spectra and Fe K-edge x-ray absorption near edge structure spectra (XANES) of the samples, in combinations with Tauc plots of the UV–vis absorption spectra. The trace element content of the samples was analyzed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). As a result, iron impurity in the samples has been confirmed as Fe3+ by XANES spectra, and hence, revealed as the cause of yellow color in natural yellow sapphire samples. Besides, the absorptions at 423 nm, 457 nm, 487 nm and 553 nm and emissions at 609 nm and 841 nm of Fe3+-Be2+ mixed donor states were detected by UV–vis excitation, which is the novel finding on the origin of yellow coloration in beryllium-treated sapphires. Therefore, an energy band model for mixed Fe3+-Be2+ donor states is proposed to be responsible for the yellow color center in beryllium-treated yellow sapphires, comparable to Fe3+ and Fe3+/Fe3+ states for the natural yellow sapphires commonly contain high iron.