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Hypertension (HT) is a common chronic condition linked to increased cardiovascular risk, reduced functional capacity, altered muscle properties, and impaired psychosocial well-being. Therefore, this study aimed to compare the 12-week effects of chair-based yoga and manual therapy on cardiovascular, functional, musculoskeletal, and psychosocial outcomes in individuals with HT. This single-blinded, randomized controlled trial included 75 participants (48 females) who were randomly allocated to three groups: Group I (Patient Education-PE), Group II (PE+Chair Yoga), and Group III (PE+Manual Therapy). Interventions were conducted twice weekly for 45 min over 12 weeks. Outcome measures included systolic and diastolic blood pressure (SBP/DBP), heart rate (HR), the 6-Minute Walk Test, muscle tone and stiffness (Myoton PRO), anxiety and depression, and mental well-being. Both Group II and Group III led to significant within-group reductions in SBP (p = 0.02 and p = 0.03, respectively) and HR (p = 0.04 and p = 0.02, respectively), with significant group-by-time interactions favoring Groups II and III over Group I. Functional capacity improved significantly in Groups II and III compared to Group I (p = 0.04). Group III specifically demonstrated significant reductions in muscle tone (p = 0.03) and stiffness (p = 0.04). Group II showed superior improvements in anxiety scores (p = 0.04) and mental well-being compared to other groups. Chair-based yoga and manual therapy are effective non-pharmacological strategies for enhancing autonomic regulation and reducing blood pressure in hypertensive patients. While both interventions improve cardiovascular and functional parameters, manual therapy is more effective for modulating muscle viscoelastic properties. In contrast, chair yoga provides greater benefits for psychosocial well-being and anxiety reduction.