Background The COVID-19 pandemic has been associated with various autoimmune manifestations. Several studies have suggested a potential association between COVID-19 and thyroid diseases (TDs); however, findings remain inconclusive and are primarily based on relatively small studies. Population-level data examining the differential impact of the pandemic on specific thyroid conditions are scarce. Objective To examine the incidence patterns of Hashimoto’s Thyroiditis (HT), Graves’ Disease (GD), and Subacute Thyroiditis (SAT) during the COVID-19 pandemic compared to the pre-pandemic period. Methods We conducted a population-based retrospective cohort study using interrupted time series analysis of adults (≥16 years) in the Clalit Health Services southern district of Israel from January 2018 to December 2022. New cases of TDs were identified using either ICD-9 codes, laboratory results, medication dispensing data or a combination of them. Monthly disease-specific incidence rates were compared between pre-pandemic (January 2018-February 2020) and pandemic (March 2020-December 2022) periods, with adjustment for seasonal variations. Results Among 4,765 incident TD cases identified, 3,731 (78.3%) had HT, 698 (14.6%) had GD, and 336 (7.1%) had SAT. The mean age was similar across groups (43–45 years) with consistent female predominance (77%). Interrupted time series analysis revealed a significant 30% increase in HT incidence during the pandemic period (IRR 1.30, 95% CI 1.04-1.64, p=0.023), which began prior to the national vaccination campaign. GD showed a non-significant upward trend suggestive of a possible increased incidence (IRR 1.66, 95% CI 0.99-2.79, p=0.054). Conversely, SAT demonstrated a significant 54% reduction in incidence (IRR 0.46, 95% CI 0.21-0.99, p=0.049). Conclusions The COVID-19 pandemic was associated with a significant increase in HT incidence and an unexpected decrease in SAT. These findings highlight the heterogeneous impact of the pandemic on different TDs.