Tobler will leave the company on June 14 after joining as CFO in April 2014.
Both chairman Russell Ball and CEO João Carrêlo wished him well in his unspecified future endeavours.
Lydian said it would begin the search process for a replacement in due course.
The company has had issues in starting up its Amulsar gold project in Armenia, where development has been "illegally blockaded" since June 2018.