Hashimoto’s thyroiditis (HT) is a chronic autoimmune thyroid disease caused by the interaction between genetic and environmental factors. There is a wide range of clinical manifestations, and since most patients develop hypothyroidism over time, lifelong levothyroxine replacement therapy is required in most cases. The role of nutrition in HT management is usually neglected. Nutritional therapy in people with HT is based on an anti-inflammatory diet that can positively contribute to the regulation of the immune system and the achievement of the desired body weight. The study involved 73 (5 M and 68 F) subjects diagnosed with HT who were recruited from the Outpatient Endocrinology Clinic or the Outpatient Clinic for Thyroid Diseases of the Nuclear Medicine Department at University Hospital Center Rijeka. The average age of the respondents is 48 years, and the average body mass index is 33.1 kg/m2. The aim of the study was to determine the relationship between eating habits, body weight and thyroid function in people with HT. A FFQ (food frequency questionnaire) survey model was used to estimate daily micronutrient intake. The following variables were tested: serum thyrotropin (TSH), free thyroxine (fT4), C-reactive protein (CRP), anti-thyroid peroxidase antibody (anti-TPO) titer, average daily selenium and iodine intake, and body mass index (BMI). The average daily iodine intake was found to be 55% lower and the selenium intake 40% lower than recommended. Although no significant correlation was found between iodine and selenium intake with serum TSH, fT4, and CRP concentrations, a growing trend of average daily iodine intake and average daily selenium intake was observed with increasing anti-TPO antibody titers. The highest intake of these micronutrients was recorded in the group of subjects with the highest anti-TPO antibodies titers. No correlation was found between BMI and TSH and fT4 serum concentrations, but a moderately to high correlation between BMI and CRP serum levels was found. The highest titer of anti-TPO antibodies was also found in the subjects with the highest level of obesity.