Charity Reading Pride called for a boycott of the site over the company's reported historic donations to anti-LGBT+ organisations.
The chicken chain opened in Reading's Oracle shopping centre on 10 October, but a spokesperson for the centre told the BBC it has now decided not to extend the company's lease beyond its six-month pilot period.
Chick-fil-A was founded in 1967 and operates over 2,000 sites in North America.
It faced a boycott in the US after its CEO made comments opposing same-sex marriage in 2012, and has been criticised for past donations to organisations with alleged anti-LGBT+ policies.
The company says it has “no social or political agenda” and focuses its charitable donations on youth and education programmes.
Reading Pride says in a statement: “In conversation with The Oracle, we have been told that Chick-fil-A will not trade beyond its current six-month pilot period.
“The Oracle management have also stated they will review their selection process and ensure a more thorough check is in place.
“The reason for allowing [Chick-fil-A] to remain for six months is to allow for re-settlement and notice for employees that have moved from other jobs.”
A planned peaceful protest against the restaurant chain organised by Reading Pride will still go ahead on 19 October.
A Chick-fil-A spokesperson says: “Chick-fil-A is always evaluating potential new locations in the hope of serving customers great food and award winning service. This six-month pilot licensed location was part of our exploration in international markets.”