Hashimoto's thyroiditis is an autoimmune disease in which thyroid cells are attacked through cell-and antibody-mediated immune processes. A gluten-free diet reduces antibody concentration and regulates thyroid autoimmunization. Mediterranean diet reduces oxidative stress. This study evaluates the short-term effects of Mediterranean, gluten-free, and Mediterranean gluten-free dietary patterns on thyroid function and autoantibody levels of patients. The 40 patients with Hashimoto's thyroiditis included in the study were randomly divided into four groups (defined as gluten-free, Mediterranean, Mediterranean gluten-free, and controls) for 12 weeks. Thyroid function tests, autoantibody levels, and food consumption were recorded at the beginning and end of the study. There was no statistically significant difference in TSH levels of the groups before the intervention, but a statistically significant difference was found afterward (p < 0.05). Free T3 hormone levels showed a statistically significant difference across the groups before and after the intervention (p < 0.05). Free T3 hormone levels increased significantly in all intervention groups after the intervention, with the highest increase in the Mediterranean group (p < 0.05). In the intervention groups, anti-TPO and anti-Tg levels decreased after the intervention; however, this difference was not significant across groups (p > 0.05). In addition, body weight, body mass index, waist and hip circumference averages decreased significantly in all intervention groups compared with controls (p < 0.05). The study achieved an increase in Free T3 hormone levels in the intervention groups. The most marked difference was seen in the Mediterranean gluten-free diet model, which may be due to the anti-inflammatory effect of both Mediterranean and gluten-free diets and the loss of body weight as a result of the intervention.