Francisco entered 2013 as the replacement for the recently retired Chipper Jones at third base, along with Chris Johnson. On April 16, 2013, Francisco had his first career multi-homer game in a 6–3 win over the Kansas City Royals. On May 8, Francisco hit his first career grand slam against Reds pitcher J. J. Hoover (who he had been traded for). Francisco was designated for assignment by the Braves on May 30 to make room on the roster for Alex Wood. At that point, Johnson won the starting third base job for himself. In 35 games with Atlanta, Francisco hit .241/.287/.398 with 5 HR and 16 RBI.
On June 3, 2013, Francisco was traded by the Braves to the Milwaukee Brewers for minor league pitcher Tom Keeling. He split first base duties with Yuniesky Betancourt until around mid-August, when Jonathan Lucroy and Sean Halton got more starts, with Francisco getting the smallest third, being used more often as a pinch-hitter. In 124 total games, he hit .227/.296/.412 with 18 HR and 48 RBI. He was released on March 24, 2014.