The Arizal was Ashkenazi. He davened in an Ashkenazic Shul in Tzefas at key times of the Jewish year, such as the ימים נוראים and רגלים, as well as at other times, and darshened there as well.
He is referred to over and over again, by his contemporaries, as the אשכנזי רבי יצחק. The moniker אר”י, by which he is known, stands for אשכנזי רבי יצחק.