McEwan will be joined at Loch Park by his assistants Craig Potter and Stevie Kerrigan.
The trio had only been in charge for 15 weeks having taken over from Gavin Duncan in October but achieved an upturn in results to have Arthurlie looking up the table.
John Stewart, Glens secretary, explained in a statement on the Glenafton website: "It has been a thorough process and the club has been overwhelmed with the quality of applications.
"It was a very difficult decision to make but we have decided to go with Craig’s team all of whom have been involved in football at professional level and in the junior game for numerous years now.
"It was also a big factor that all three were involved with the club in the past and know our aims and ambitions.
"The club would like to thank all the other applicants for their applications and hope they understand why we came to this decision.
"Finally I would like to thank Arthurlie for giving us permission to speak to Craig McEwan regarding the vacant managerial position."
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