Indirect interspecific effects (IIEs) occur when one species affects another through a third intermediary species. Understanding the role of IIEs in population dynamics is key for predicting community-level impacts of environmental change. Yet, empirically teasing apart IIEs from other interactions and population drivers has proven challenging and data-demanding, particularly in species-rich communities. We used stochastic population models parameterized with long-term time series of individual data to simulate population trajectories and examine IIEs in a simple high-arctic vertebrate food chain consisting of the wild Svalbard reindeer, its scavenger (the Arctic fox) and the barnacle goose, a migratory prey of the fox. We used the simulated population trajectories to explore co-fluctuations between the species within the food chain. Additionally, we adjusted the model in two ways: first, to isolate the impact of fluctuations in the abundance of a species by keeping its abundance constant; and second, to isolate the impact of a trophic interaction on the dynamics of other species by setting the abundance of the influencing species to zero. We found that fluctuations in reindeer carcasses shaped fox abundance fluctuations, which subsequently affected goose population dynamics. Reindeer and goose population growth rates were nevertheless only weakly correlated, probably in part due to demographic and environmental stochasticity, density dependence and lagged dynamics in the geese. However, removing the fluctuations in reindeer abundance or setting reindeer abundance to zero indeed demonstrated strong underlying IIEs on goose population dynamics and extinction probability. This study thus highlights the importance of species interactions, including IIEs, on species coexistence and communities in the long-term, that is beyond immediate effects and covariation in short-term fluctuations.