In June 2008, after playing 26 games in a season and a half, he underwent back surgery to repair a prolapsed disc, missing the remainder of the year. He returned the following season to have one of his best seasons, earning 10 Brownlow Medal votes to be the equal leader for Essendon and finishing fifth in the club's best and fairest award.
He tore his ACL in the opening quarter of round four and underwent a knee reconstruction, robbing Essendon of pace and skill. It was a huge loss for the Bombers, who had counted on the speedy 27-year-old to provide important pressure inside 50. In 2010, he finished third in the clubs best and fairest and was a valued commodity at the club.
Having torn his anterior cruciate ligament in round four of 2011, it took until round 18 of the 2012 season for Winderlich to make his AFL return. However on-going hamstring strains prolonged his absence and, in his second game back, against Adelaide at Football Park, he again tore the muscle. It was a bitter blow for Winderlich, who was playing his 100th game and had kicked four goals in an encouraging showing.
Winderlich continued to be a week-to-week proposition in 2013, as the midfielder turned goal-sneak remained one of Essendon’s classiest players. In full flight, he added speed and precision skills to the Bombers forward line.