The Reverend Janine Arnott was appointed to St Oswald's, in Malpas, near Whitchurch, in 2022 but some church members raised concerns about decisions over prayers and readings and the treatment of some parishioners.
At one point, flyers were stuck to Chester Cathedral in an attempt to get bishops to intervene.
The Bishop of Birkenhead, Julie Conalty, said the diocese hoped to offer constructive recommendations that would help shape and support the local church community.
"An independent reviewer has been invited to carry out a church health check, following some challenges earlier this year that were noted in the press," Bishop Conalty said.
"The aim is to build a clear picture of how things are going, and to offer constructive recommendations that will help shape and support the ongoing ministry in Malpas, Threapwood and Bickerton."
Choir member Liane Smith, who has been in the congregation for 10 years, previously told the BBC that Dr Arnott had done "a great job" when she started.
Ms Smith added: "It seems from the start of 2023, she decided things needed to change, as if sort of 'well, I've done it their way for six months and things need to change now.'"
She said it started with apparent disagreements about the choir when the rector asked them to stop singing for two weeks.
Then there were disagreements about prayers and readings, with the bell ringers stopping over allegations about the way the rector was treating some people, causing some to leave.
"It's quite a massive dismantling of a successful church community," she said.