Bexley LBC chief executive Gill Steward is to leave the council “due to a change in her personal circumstances”.
Ms Steward, who joined Bexley in 2016, will leave at the end of August.
Deputy chief executive Paul Moore will act as interim chief executive “until permanent arrangements can be put in place”, a council statement said.
It added council leader Teresa O’Neill (Con) “agreed that it was in the best interests of all parties that new leadership arrangements be put in place” after her party significantly increased its majority at May’s election.
Ms Steward said: “I’m very sad to be leaving Bexley but it is the right decision for me and for the new administration.
“I look forward to seeing the ambitious strategies and plans to which I have contributed improving the lives and opportunities of people in Bexley.”