Potential relationships between the structure of the digestive microbiota and contextual parameters were investigated by applying a multivariate variation partitioning approach. Biological variation of the digestive microbiota was significantly linked to the pure effect of diet composition (adjusted R2 = 5.4%, P < 0.05). Sampling dates, the combined effect of abalone and algal composition, the combined effect of algal composition and sampling dates, and the effect of the three explanatory variables together also explained the structuring of the microbial community (adj. R2 = 2.2%, 7.4%, 12.2%, 2.5%, respectively, Additional file 1: Figure S4). Overall, 30.8% of the biological variation of the microbial community structure was explained by abalone characteristics, algal composition, and sampling dates (P < 0.001, Additional file 1: Figure S4). The remaining 69.2% of the biological variation not explained by the selected model suggests the effect of additional variables not included in this analysis. Still, our analysis clearly demonstrates a relationship between algal diet composition, sampling dates, and the structure of the digestive microbiota.