Mixotrophic organisms are increasingly recognized as important components of ecosystems, but the factors controlling their nutrition pathways (in particular their autotrophy–heterotrophy balance) are little known. Both autotrophy and heterotrophy are expected to respond to density‐dependent mechanisms but not necessarily in the same direction and/or strength. We hypothesize that the autotrophy–heterotrophy balance of mixotrophic organisms might therefore be a function of population densities. To investigate this relationship, we sampled mixotrophic jellyfish holobionts (host, Mastigias papua etpisoni; symbiont, Cladocopium sp.) in a marine lake (Palau, Micronesia) on six occasions (from 2010 to 2018). Over this period, population densities varied ~100 fold. We characterized the nutrition of the holobionts using the δ13C and δ15N signatures as well as C:N ratios. δ13C values increased and δ15N values decreased with increasing population densities (respectively, R2 = 0.86 and 0.70, P < 0.05). Although less distinct, C:N ratios increased with increasing population densities (R2 = 0.59, 0.1 > P > 0.05). This indicates that the autotrophy–heterotrophy balance tends toward autotrophy when population densities increase. We propose that the availability of zooplanktonic prey is the main driver of this pattern. These results demonstrate that the autotrophy–heterotrophy balance of mixotrophic jellyfishes can be tightly regulated by density‐dependent mechanisms.