I now that we can use the adonis function to look at a multivariate model, in which we are able to adjust our model for several covariates. Just wondering if it is possible to generate an “adjusted” PCoA plot based on the same model?
PCoA plots are not a model per se that can be adjusted, they are a type of data-reduction ordination method and by themselves are not hypothesis-testing, unlike adonis. As so there is no adjusting the plots in a way a linear model would be, aside from changing their colors, shapes etc. You should consider PCoA and Adonis/permanova/permadisp etc as separate but complementary entities.