Forest loss is a major environmental threat in the Anthropocene. Repercussions are rarely localised and often impacts adjacent ecosystems. For example, forest loss is generally detrimental to freshwater biodiversity. There are however, some uncertainties about its effects on food webs and ecosystem functioning. We tracked changes in the food webs of four tropical stream catchments (two time points separated by a ~20-year interval) affected by varying degrees of forest loss. Our data show that the proportion of assimilated terrestrial organic matter (allochthony) remained largely invariant, but changes in food chain lengths inferred from the trophic positions of apex predators (TP) differed between catchments. Here, we found that higher rates of forest loss resulted in more significant reductions in TP. We speculate that the mechanisms involved are unrelated to diminished terrestrial subsidies as allochthony values were low (~7%) and did not shift in response to forest loss.