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Abstract Background Hashimoto’s thyroiditis is associated with serious alterations in serum lipids and glucose homeostasis. The aims of the current study were to evaluate the effect of powdered Nigella sativa on serum lipids, glucose homeostasis and anthropometric variables in patients with Hashimoto’s thyroiditis. Methods Forty patients with Hashimoto’s thyroiditis, aged between 22 and 50 years old, participated in the trial and were randomly allocated into two groups of intervention and control receiving powdered Nigella sativa or placebo daily for 8 weeks. Serum lipids, glucose homeostasis, and anthropometric variables were evaluated at baseline and after intervention. Results Treatment with Nigella sativa significantly reduced body weight and body mass index (BMI). Serum concentrations of low density lipoprotein cholesterol (LDL) and triglyceride (TG) also decreased in Nigella sativa-treated group after 8 weeks; while serum high density lipoprotein cholesterol (HDL) significantly increased after treatment with Nigella sativa (P < 0.05). None of these changes had been observed in placebo treated group. Serum Nesfatin-1 concentrations was in inverse relationship with serum triglyceride (TG) (r = − 0.31, P = 0.04). Conclusions Giving attention to the potent beneficial effects of powdered black cumin seeds in improving serum lipid profile and anthropometric features in patients with Hashimoto’s thyroiditis, this medicinal plant could be considered as a beneficial herbal supplement alongside with the disease- specific medications including Levothyroxine in management of Hashimoto’s thyroiditis- related metabolic abnormalities. Trial registration Iranian registry of clinical trials (registration number IRCT2014090819082N2- Registered 2014-09-29).