Ofcom made the announcement in a statement on their website on Wednesday.
The media watchdog, which regulates television and radio, has said it has already “laid the foundations” to improve support for LGBTQ+ employees and therefore does not need the Diversity Champions programme.
They added: “In recent months there has been significant scrutiny of some of Stonewall’s policy positions.
"In Ofcom’s case, we have considered whether our relationship with Stonewall poses a conflict or risk of perceived bias.
"Stepping back from the Diversity Champions programme, in light of this, is the right thing to do.
"As the communications regulator, an important part of our responsibility is to ensure we remain impartial and independent at all times.
“Our commitment to supporting the rights and freedoms of LGBTQ+ people is as strong as ever.
"We will continue to participate in the Stonewall Workplace Equality Index, which is widely recognised as a strong benchmarking tool for employers to measure their progress on LGBTQ+ inclusion in the workplace.”
Stonewall is a LGBTQ+ charity in the UK whose Diversity Champions programme ensures “all LGBTQ+ staff are free to be themselves in the workplace”.
The charity’s website says it works with more than 900 organisations across the country.
A Stonewall spokesperson said: “We respect Ofcom’s decision and will continue to work with them in their role as the UK’s communication regulator.
"It is sad, however, that involvement in a programme that supports an inclusive workplace for LGBTQ+ employees should be in any way regarded as an unimpartial act.
“As with every membership programme, organisations come and go depending on what works best for their inclusion journey at the time, and we’re very proud of the work we’ve done with Ofcom and wish them the best in their ongoing efforts to support all of their LGBTQ+ employees.
"It’s a simple human right that everyone, including LGBTQ+ staff, is free from discrimination and prejudice at work, and our Diversity Champions programme is one way for organisations to be supported in this.”