Bautista was to be the Pirates' starting third baseman and backup outfielder in 2008. From June 14 to 24, he hit five home runs in a span of nine games against interleague opponents Baltimore, Chicago White Sox, Toronto Blue Jays, and the New York Yankees. However, he struggled offensively for most of the year, and after the 2008 trade deadline Bautista lost his starting job to the newly acquired Andy LaRoche. Bautista was optioned to the Triple-A Indianapolis Indians on August 13.