Hi @evon,
Welcome to the forum!
Here is an example of this using Qiime2r to import an ordination artifact from Qiime2.
In short you'll just need to use the xlab and ylab
xlab(paste(round(100*ord$data$ProportionExplained[1],2),"%")) +
ylab(paste(round(100*ord$data$ProportionExplained[2],2),"%")) +