Temporal variability in primary productivity can change habitat quality for consumer species by affecting the energy levels available as food resources. However, it remains unclear how habitat quality fluctuations may determine the dynamics of spatially structured populations, where the effects of habitat size, quality, and isolation have been customarily assessed assuming static habitats. We present the first empirical evaluation on the effects of stochastic fluctuations in primary productivity —a major outcome of ecosystem functions— on the metapopulation dynamics of a primary consumer. A unique 13-year dataset from an herbivore rodent was used to test the hypothesis that inter-annual variations in primary productivity determine habitat occupancy patterns and colonization and extinction processes. Inter-annual variability in productivity and in the growing season phenology significantly influenced habitat colonization patterns and occupancy dynamics. These effects lead to changes in connectivity to other potentially occupied habitat patches, which then feedback into occupancy dynamics. According to the results, the dynamics of primary productivity accounted for > 50% of the variation in occupancy probability, depending on patch size and landscape configuration. Evidence connecting primary productivity dynamics and spatial population processes has broad implications for metapopulation persistence in fluctuating and changing environments.