Alpine streams can exhibit naturally high levels of flow intermittency. However, how flow intermittency in alpine streams affects ecosystem functions such as food web trophic structure is virtually unknown. Here, we characterized the trophic diversity of aquatic food webs in 28 headwater streams of the Val Roseg, a glacierized alpine catchment. We compared stable isotope (δ13C and δ15N) trophic indices to high temporal resolution data on flow intermittency. Overall trophic diversity, food chain length, and diversity of basal resource use did not differ to a large extent across streams. In contrast, gradient and mixing model analysis indicated that primary consumers assimilated proportionally more periphyton and less allochthonous organic matter in more intermittent streams. Higher coarse particulate organic matter (CPOM) C:N ratios were an additional driver of changes in macroinvertebrate diets. These results indicate that the trophic base of stream food webs shifts away from terrestrial organic matter to autochthonous organic matter as flow intermittency increases, most likely due to reduced CPOM conditioning in dry streams. This study highlights the significant, yet gradual shifts in ecosystem function that occur as streamflow becomes more intermittent in alpine streams. As alpine streams become more intermittent, identifying which functional changes occur via gradual as opposed to threshold responses is likely to be vitally important to their management and conservation.