Mucosa-associated lymphoid tissue (MALT) lymphoma is an indolent B-cell non-Hodgkin lymphoma that typically arises in mucosal tissues, most commonly in the stomach, but also in the salivary glands, thyroid, lungs, orbits, and skin. Laryngeal MALT lymphoma is extremely rare, particularly in the subglottic region. We report a rare case of subglottic MALT lymphoma that was diagnosed in a 73-year-old woman with a history of Sjögren’s syndrome, interstitial pneumonia, and Hashimoto’s thyroiditis. The patient presented with progressive exertional dyspnea. CT imaging revealed a smooth, subglottic mass and an enlarged thyroid gland. Despite multiple biopsies over a 10-month period, a definitive diagnosis proved elusive due to limited tissue availability and similarity of findings to those of a benign lymph node. The final diagnosis of MALT lymphoma was confirmed by immunohistochemistry in the ninth biopsy, which showed a decrease in the density of CD20-positive cells and proliferation of CD138-positive plasma cells with lambda light chain restriction, suggesting differentiation of CD20-positive cells into CD138-positive plasma cells and confirming clonality. Recognition of the indolent clinical progression of MALT lymphomas combined with immunohistochemical analysis was critical for obtaining the diagnosis. Due to the presence of underlying interstitial pneumonia, which contraindicates radiotherapy, the patient received rituximab monotherapy. The tumor responded well to treatment, and no recurrence has been observed for over two years. Persistent and repeated biopsies, as well as close collaboration with hematologists, are essential in such cases. In patients with unexplained respiratory symptoms and autoimmune backgrounds, subglottic or tracheal tumors should be considered in the differential diagnosis. This case shows how difficult it can be to diagnose a MALT lymphoma in the subglottic area and why repeated biopsies are sometimes necessary.