With the election of the Abbott Coalition government in September 2013 he was appointed Minister for Industry. He was later sworn in as the Minister for Industry and Science on 23 December 2014. Upon the ascension of the Turnbull Government in September 2015, he was dropped from the new ministry despite being a Turnbull supporter. On 3 December 2015, Macfarlane announced his intention to sit with the federal Nationals. He claimed that his experience representing regional interests was "second only to" retiring federal Nationals leader and fellow Queenslander Warren Truss. Although local party members overwhelmingly supported Macfarlane's decision, the Liberal National Party of Queensland executive blocked the move. LNP officials said that even with the overwhelming support of LNP members in Macfarlane's seat, "the interests of our party beyond his electorate" required that Macfarlane stay in the Liberal party room.