1. The relative contributions of habitat and food availability on fitness may provide evidence for key habitat features needed to safeguard population persistence. However, defining habitat quality for a species can be a complex task, especially if knowledge on the relationship between individual performance and habitat quality is lacking. 2. Here, we determined the relative importance of availability of suitable forest habitat, body mass, and food from masting tree species on female lifetime reproductive success (LRS) of Siberian flying squirrels (Pteromys volans). 3. We calculated LRS of 500 female flying squirrels based on a 22 year-long longitudinal data set of two populations from western Finland. We assessed with generalised additive models the potential effects of availability of suitable habitat and cumulative lifetime availability of food from masting tree species on female LRS, longevity and fecundity. On a reduced dataset, we evaluated the importance of female winter body mass and conducted a piecewise path analysis to determine how variables were connected. 4. According to generalised additive models female longevity, fecundity and LRS were mainly determined by variation in cumulative lifetime availability of food from masting alder and birch. Instead, habitat and body mass had smaller role. The path analysis indicated that lifetime food availability had direct effect on longevity and fecundity, and these had equal effect on LRS at both study sites. 5. Our results on LRS shows that the occurrence of tree masting events during a flying squirrel female’s lifetime have profoundly larger effect on lifetime reproductive success than the cover of suitable forest habitat. Furthermore, this study emphasises the importance of both fecundity and longevity, and the indirect effects of food availability via those components, as determinants of lifetime fitness of female flying squirrels.