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Up to 5 % of the general population may have hypothyroidism (HT), with an additional 5 % thought to remain undiagnosed. This study assessed the effect of integral yoga intervention (IYI) on thyroid profile (thyroid stimulating hormone: TSH, triiodothyronine: T3, and thyroxine: T4), metabolic profile (high-density lipoprotein: HDL, low-density lipoprotein: LDL, triglycerides: Tg, total cholesterol: Tc, and body mass index: BMI), mono medication (levothyroxine: LT4) dependence, and comorbid daytime sleepiness and depression in adult females with HT. Sixty-two female participants with TSH levels above normal range and age (mean ± SD: 41.48 ± 6.2) were recruited from AIIMS Rishikesh, Uttarakhand, India, before random allocation into an equal-sized control group (CG) and yoga group (YG). Participants in the YG received a three-month online IYI (5 days/week, 60 min/session, totalling 60 sessions) due to COVID-19 regulatory restrictions, in addition to their prescribed LT4. Split-plot ANOVA with Benjamini-Hochberg-adjusted post hoc tests for inter- and intra-group comparisons was computed to assess between-group, within group and interaction effects and ascertain trends. Three-month online IYI significantly (p < 0.001) improved TSH (0.63), T3 (1.08), T4 (-0.79), LT4 (-2.80), Tc (-3.10), LDL (0.85), HDL (2.84), Tg (-3.24), BMI (-1.53), day time sleepiness (-2.83), and depression (-1.85) of the YG participants compared to their controls. Post-intervention improvements in thyroid profile, metabolic profile, mono medication dependence, and comorbid daytime sleepiness and depressive symptoms in the YG participants compared to their controls indicated yoga as a low-harm, affordable, scalable, and accessible add-on therapy for HT.