Background: Indeterminate fine-needle aspiration cytology (FNAC) imposes challenges in the management of thyroid nodules. This study aimed to examine whether preoperative anti-thyroid antibodies (Abs) and TSH are indicators of thyroid malignancy and aggressive behavior in patients with indeterminate FNAC. Methods: This was a retrospective study of thyroidectomy patients from 2008 to 2016. We analyzed Abs and TSH levels, FNAC, and histopathology. Serum antibody levels were categorized as ‘Undetectable’, ‘In-range’ if detectable but within normal range, and ‘Elevated’ if above upper limit of normal. ‘Detectable’ levels referred to ‘In-range’ and ‘Elevated’ combined. Results: There were 531 patients included. Of 402 patients with preoperative FNAC, 104 (25.9%) had indeterminate cytology (Bethesda III–V). Of these, 39 (37.5%) were malignant and 65 (62.5%) benign on histopathology. In the setting of indeterminate FNAC, an increased risk of malignancy was associated with ‘Elevated’ thyroglobulin antibodies (TgAb) (OR 7.25, 95% CI 1.13–77.15, P = 0.01) and ‘Elevated’ thyroid peroxidase antibodies (TPOAb) (OR 6.79, 95% CI 1.23–45.88, P = 0.008). Similarly, while still ‘In-range’, TSH ≥ 1 mIU/L was associated with an increased risk of malignancy (OR 3.23, 95% CI 1.14–9.33, P = 0.01). In all patients with malignancy, the mean tumor size was 8 mm larger in those with TSH ≥ 1 mIU/L (P = 0.03); furthermore, in PTC patients, ‘Detectable’ TgAb conferred a 4 × risk of lymph node metastasis (95% CI 1.03–13.77, P = 0.02). Conclusion: In this cohort, in indeterminate FNAC patients, Abs and TSH were associated with an increased risk of malignancy. Additionally, TgAb and TSH were potential markers of aggressive biology. As such, they may be diagnostic and prognostic adjuncts.