We investigate the influence of mixotrophy on the dynamical properties of a six-population model of a three–trophic level Southern Ocean ecosystem. We find that including mixotrophic interactions between the lowest trophic level populations can significantly influence the dynamics of the highest trophic level populations, and in extreme cases lead to extinctions. Significantly, not only is the strength of the mixotrophic interaction important, it matters how it is included in the model, as a specialist or generalist grazer. We note in particular that the generalist formulation is inappropriate for “green” mixotrophs that fuel the majority of their growth by photosynthesis. The model can have complicated dynamics when subject to large amplitude, regular forcing, suggesting the sea ice—salps link may be obfuscated by endogenous population oscillations. Further, we observe that constructing the model within the Conservative Normal framework allows insights into the bifurcation behaviour of the model.