The Athens club have been struggling in the lower reaches of the table for most of the season and Monday's 2-0 loss at PAS Yiannina means the Yellows are one point clear of the relegation zone with two matches to play.
Lienen was appointed in October and initially guided the cash-strapped club to some positive results after they experienced their worst start to a season under Vangelis Vlachos.
But in the wake of their latest setback, the club have opted to change things ahead of Sunday's vital relegation clash against fellow strugglers Panthrakikos.
A club press spokesperson confirmed the departure, with an official statement expected later on Tuesday.
Local media said former AEK and Greece defender Traianos Dellas was the leading candidate to take over.
AEK have been operating on a shoe-string budget following a period of financial turmoil in which virtually an entire first-team squad was sold off in order to secure a licence and preserve their top-flight status.
Club officials have been seeking new investors but, after the recent collapse of a potential deal with London-based investment bank Seymour Pierce, their efforts have been unsuccessful.
The problems have not stopped there in what has been a turbulent season to forget for the club.
Groups of supporters have staged regular protests at the training facilities due to the state of the team's finances, while the controversial Nazi-salute goal celebration of midfielder Giorgos Katidis last month has also been another blow to AEK's reputation.