[6] On 17 July 2013, it was announced that Schäfer will become the new coach of Jamaica,[7] replacing previous manager Theodore Whitmore who resigned from his position following a 2–0 loss to Honduras.

Shortly after, on 22 July 2015 Schäfer's team reached the Final of the Gold Cup after beating tournament favourites the United States.

On 2 October 2017, Schäfer was chosen to become the new manager of Iranian club Esteghlal, following Alireza Mansourian's resignation as team's head coach.

[14] Upon being appointed, Schäfer re-called Esteghlal's captain Mehdi Rahmati who was banned from joining the team by the previous coach, Alireza Mansourian,[15] as well as asking the management to re-sign Behnam Barzay whose contract wasn't renewed and became a free agent in summer.

[25] In association with Esteghlal vice president Seyed Pendar Toufighi, two new signings were made by Schäfer; free agent's Bojan Najdenov and Mame Thiam arrived at the club.

[29][30] In the 2018 AFC Champions League, Schäfer's team were drawn against Al-Rayyan, Al Ain and Al-Hilal in the competition's group of death.

[32] On 1 March 2018, Schäfer won his first Tehran derby as a manager in a 1–0 victory;[33] this was also his third win against Branko Ivanković, having previously beaten him twice in 2.

He also asked to sign Nigerian striker Alhaji Gero, his compatriot Markus Neumayr as well as Iraq international Humam Tariq.

[43][44][45] Schäfer's Esteghlal were eliminated in the quarterfinals of the AFC Champions League after a 5–3 aggregate loss to Al Sadd on 17 September 2018.

[47] On 29 April 2019, Schäfer was suspended until the end of the season two days after Esteghlal's loss to Padideh in the league and replaced by his assistant Farhad Majidi.

[48][49] On 6 July 2019, Schäfer was confirmed as the new manager of Emirati side Baniyas,[50] he coached the team until his contract expired with barely any notable records other than getting to the UAE President's Cup semi finals.