Yes, you can. I know because I played with Fisher's iris data set a little bit, and I can tell you that the App is capable of solving multi-class problems.
Sorry, my answer was a bit short. For Fisher's iris data set:
fisherTable = table(meas, species)
For solving multi-class problems in the App, the best way is to use a table, with all your predictors as the first p columns, and the labels as the last (in that case, the labels are strings).
Open the App, select 'New session', 'From the workspace'. Select fisherTable in Section 1, and Section 2 should look like this:
So the meas are predictors, and the species are the response. Choose your validation method in Section 3 and you should be good to go! This should work for any 3-class data set.