Born in Kazakhstan to Russian parents of German ancestry, Merkel moved to Germany with them in 1998, aged 6. There he started playing football with amateur team JSG Westerwald, before joining VfB Stuttgart at the age of 11. In 2008, he moved to Italian side Milan. During his time in the club's youth system, he was a member of the under-20 side who won the Coppa Italia Primavera in 2010, 25 years after the team's last success in the competition.

Merkel received his first call-ups for the senior team during the 2009–10 campaign, but he was never fielded nor named on the bench. At the beginning of the following season, he took part in some pre-season games, putting up good performances. Merkel eventually made his first-team official debut on 8 December 2010, coming off the bench in a UEFA Champions League group stage game against Ajax. A month later, on 6 January 2011, he also made his league debut, figuring in the starting line-up for a match against Cagliari. Merkel went on to score his first professional goal on 20 January, as Milan pulled off a 3–0 win over Bari in the Coppa Italia round of 16.