His departure had been anticipated after failure to reach the Twenty20 finals following a play-off defeat by Holland in November.
It was then revealed that former England all-rounder Paul Collingwood would jointly lead the Scots into the World Cup qualifiers, stepping up from his role as assistant to take the team along with former Scotland captain Craig Wright.
Steindl spent six years in charge and his exit brought to an end 19 years continuous association with the national governing body as both an employee and a volunteer.
He said: "The decision to step down has been a difficult one but I feel it is the right one for the team's immediate future.
"I have enjoyed the challenges that the job has involved and feel privileged to have worked in this role for the last six years.
"I have been lucky enough to work with some very good cricketers in this time and I take particular pride in overseeing and helping establish Scotland's first professional structure.
"I hope this system will be built upon and improved in years to come.
"Thanks must go to my support staff and team captains, past and present, who have played an enormous role in my life over the six years.
"In particular thanks must be extended to Tony Judd, Michael Powell, Toby Bailey, Mhairi MacPhail, Simon Smith and latterly Paul Collingwood.
"Not only have they been outstanding professionals but also become my good friends.
"I will always treasure the special memories of singing 'Flower of Scotland' after every win with my team-mates.
"I am looking forward to having the opportunity to spend some time with my family, who have supported me and sacrificed much over the six years I have been head coach before I look for my next challenge.
"I wish the team every success in the future."
Cricket Scotland chief executive Roddy Smith added: "Peter took on the national team at a transitional time and has worked tirelessly to improve the team individually and collectively.
"His decision to step down from the role at this time, in his belief that this is in the best interest of the team, shows his commitment to the squad and his desire that they succeed.
"I would like to publicly thank him for his effort, commitment and professionalism during his time as head coach of the Scotland cricket team."