In 2014, Lijnders moved to Liverpool as development coach under Brendan Rodgers, and later continued with Jürgen Klopp as assistant coach, as well as first team trainer with Klopp.[2]
On 2 January 2018, Lijnders accepted the managerial job at NEC in the Dutch Eerste Divisie, signing a year and a half long contract.[3][4] On 17 May 2018, Lijnders was sacked after NEC failed to gain promotion to the Eredivisie in the promotion play-offs.[5]
In 2022, Lijnders published his first book, Intensity: Our Identity, an inside account of Liverpool's 2021–22 season.[7] Later that year, with the club struggling for form the following season, Lijnders was forced to defend himself against accusations that his book had "exposed" Liverpool's secrets.[8][9]
On 26 January 2024, it was announced that, along with Jürgen Klopp, he would be leaving Liverpool at the end of the season.[10] Lijnders was expected to pursue his own managerial career when he leaves.[11]
On 15 May 2024, Lijnders signed on as the new Red Bull Salzburg manager with a contract valid until June 2027.[12] Early in the 2024-25 season, Lijnders faced criticism after he demoted Austria's national team goalie Alexander Schlager to the bench, fielding Leipzig loan Janis Blaswich. Blaswich allowed 12 goals in Sazburg's first three Champions League games.[13] On 16 December 2024, it was announced that Salzburg were parting ways with Lijnders after just 29 games in charge of the club with Salzburg chasing a 10-point deficit in the Bundesliga.[14]