This study investigated the mountain food systems in the Hindu Kush Karakoram Pamir Landscape (HKPL) in Pakistan. It analyzed the impacts of climate change on agriculture and livestock and identified key opportunities which can be tapped into to improve sustainability in food systems. The study applied a “multiple case studies approach” and collected data from four study sites at different altitudes, using the method of slow focus group discussions, key informant interviews, and non-participant observation. Findings revealed that the contribution of local agriculture and livestock to people’s food consumption has gradually declined, increasing their dependence on external food items. Local food systems are losing diversity, which has negatively impacted people’s dietary diversity. The youth has lost interest in agriculture due to low productivity and profitability in a high altitude village—Misgar (≈3200 m above sea level). In all sites, local people perceived mixed impacts (both positive and negative) of climate change on food systems. Climate change together with enhanced use of pesticides and inorganic fertilizers, high yielding seed, and improved farm management have positive, and climate-attributed increase in crop pest attacks has negative impact on crop productivity. Moreover, local people perceived negative impacts of climate change on pastures and water availability in traditional irrigation systems without significant influence on crop and livestock productivity. In food systems, these are needed to maximize benefits from the local potential for organic production, livestock integration, value chain development, traditional food crops, medicinal plants, and protected vegetables cultivation to reduce the vulnerability of food systems to climactic and economic shocks, and improve the sustainability.