Climate change is creating hotter, drier, and more extreme weather. Weather anomalies such as extended drought along the Pacific Coast of North America are redefining ecosystems. In the Sierra Nevada mountains of California, an isolated, distinct and federally endangered population of fishers (Pekania pennanti) currently faces multiple threats. Severe drought, tree mortality, and megafires are reshaping the landscape in the southern Sierra with largely unknown effects on fisher ecology and conservation. Using hair collected during long-term population monitoring, we analyzed stable isotopes to quantify the diets of fishers before and after drought, and explored how habitat quality mediated the effect of drought on fisher diet. For the core population of fishers which occupy the northern and western portions of this region, their isotopic niche declined both in drought and in lower-quality habitats. Regardless of drought or habitat conditions, the summer diet of fishers here was dominated by fungi (47%), while little vertebrate mass (14%) was consumed. However, drought and habitat did influence consumption of plants and insects; fishers consumed more insects and less plants in drought conditions and in poorer habitat. In contrast, at the perennially dry, high-altitude Kern Plateau at the southeastern extent of their range, fishers predominantly consumed vertebrates (59%). Fishers show great plasticity in their diet, but the means and capacity for this flexibility is poorly understood. Retaining atypical diet items, notably fungi, and a diversity of forage in the Sierra Nevada could help to buffer the negative fitness costs from rapid environmental change for this endangered species.