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Indirect impacts of Human Wildlife Conflict (HWC) are largely ignored, poorly understood, and scantly reported in the literature on HWC. Subsistence farmers in the Himalayan kingdom of Bhutan experience an increasing intensification of HWC impacts. Working across four districts representing different geographic regions of the country, we explored the perceived indirect impacts of HWC and how they affect the well-being and happiness of subsistence farmers using qualitative interviews (n = 48) and focus group discussions (n = 8). We conducted a qualitative thematic analysis. Based on respondent’s explanations, we coded the data according to effect of indirect impacts on human, social, financial, physical, natural, and psychological capitals. Mental distress, constant worries about food insecurity, fears for physical safety, frustration of movement restriction due to fear of being attack by wildlife, feelings of economic insecurity and anger over loss of crop and livestock due to wild predators affect the psychological health and well-being of research participants. Vulnerabilities related to gender and wealth status further deepen the effect of indirect impacts. Policies designed to address HWC should incorporate an understanding of the effects of indirect impacts of HWC and should focus on female-headed and poor households to reduce the negative effects of wildlife impacts.