Background: Polycystic ovary syndrome (PCOS) is a complex endocrinopathy of women in their reproductive age with diversity in clinical manifestations. The phenotypic expressions and altered anthropometric indices are the key indicators of the abnormal transformations in metabolic, endocrine, and reproductive functionality of PCOS. Stress-induced activation of the Sympathetic-Adrenal-Medullary (SAM)-system and Hypothalamic-Pituitary-Adrenal (HPA)-axis results in series of neuroendocrine adaptations where over-activation of SAM/HPA response negatively affects the Hypothalamic-Pituitary-Gonadal (HPG) axis that highlight the possibility of the adverse impact of stress response system on reproductive and metabolic functions. Psychological distress and anxiety induced by the COVID-19 pandemic may aggravate the expressivity of PCOS and associated complexities. Objective: The present study aimed to find out some phenotypic features (hirsutism, acne, Acanthosis Nigricans (AN) and alopecia) in association with deviated anthropometric and derived indices, and stress biomarkers (Salivary α-amylase (SAA) and cortisol of SAM and HPA-axis respectively) among PCOS patients. Statistical analysis: SPSS (IBM, version 20) and Microsoft Office Excel 2010 were implied, and the quantitative variables were described as mean±SD (P < 0.01 and P < 0.05). Results: Significant alternations in the anthropometric indices were observed for PCOS patients that may lead to health risk. Alteration in body composition was strongly correlated with stress biomarkers in the case of both the experimental and control group. Central obesity was found to be a significant indicator of altered body composition in response to stress. Conclusion: Stress is a key modulator in the alternation of phenotypic manifestation as well as body composition of PCOS patients which could be the plausible reason for further deterioration of this multifaceted disorder due to the COVID-19 pandemic.