Stomach-content analysis is commonly used to study fish diets. For small-bodied fish, dissection is the traditional method that is used to obtain stomach contents. However, this may be unsuitable, particularly for those of conservation concern. Non-lethal methods are therefore needed to minimise harm, but relatively few validated approaches are available for small-bodied species. This study characterised the diet of Galaxias olidus, a small-bodied galaxiid, using DNA metabarcoding of two non-lethal sample types, flushed stomach contents and faecal samples. Flushed stomach contents and faecal samples were collected from the same individuals. Prey composition and richness were compared between the two sample types. Both sample types were dominated by insects (over 90% of reads), particularly Diptera, Trichoptera, Coleoptera, and Hymenoptera, although the proportions and dominance patterns of these orders varied between sample types. The most commonly detected families were Diptera, including Chloropidae, Chironomidae, Muscidae, and Culicidae in flushed stomach contents, and Chloropidae and Culicidae in faeces. Terrestrial prey made up 12–21% of reads, suggesting they were an important part of the diet. Flushed stomach contents showed a wider variety of prey than faeces (71 versus 38 taxa) and revealed more unique prey taxa (54 versus 24). Lower prey richness in faeces was likely owing to digestive processes. Despite these differences, faecal samples broadly reflected the dominant dietary signal, and the relative abundances of individual taxa did not differ significantly between the two sample types. Overall, stomach flushing provided a more complete picture of recent diet and appeared to be the more informative non-lethal approach for small-bodied galaxiids. However, faecal sampling also showed promise as a non-lethal method for detecting dominant dietary items when stomach flushing is not feasible, with both approaches having potential application to threatened small-bodied fishes.