The Trust had organised a special event at Felbrigg Hall in Norfolk, marking 50 years since the decriminalisation of homosexuality. It's part of its Prejudice and Pride campaign.
Some workers refused to wear the rainbow badge or lanyard and had been told they would have to work behind the scenes.
After days of criticism that the decision was too politically correct, the National Trust backtracked and made wearing the badge optional for volunteers.
In a statement, the conservation organisation said the purpose of the idea to wear rainbow badges was to make all visitors feel welcome.
It said: "We remain absolutely committed to our Pride programme, which will continue as intended, along with the exhibition at Felbrigg.
"However, we are aware that some volunteers had conflicting, personal opinions about wearing the rainbow lanyards and badges. That was never our intention.
"We are therefore making it clear to volunteers that the wearing of the badge is optional and a personal decision. We will be speaking to all our volunteers at Felbrigg over the coming days about this issue."
The National Trust also addressed the recent backlash it faced over "outing" Robert Wyndham Ketton-Cremer, the late owner of the Jacobean Hall, as gay.
The organisation commissioned a short film narrated by comedian Stephen Fry which featured the lives of various LGBT people who owned the Trust's properties. The people highlighted kept their sexuality private when they were alive.
Ketton-Cremer's relatives wrote to The Daily Telegraph complaining that the "intensely private" historian and poet, who died 48 years ago, shouldn't have been exposed as homosexual.
The National Trust said: "We are using the 50th anniversary of the partial decriminalisation of homosexuality as an opportunity to tell the stories of the people at some of our places, whose personal lives were outside the social norms of their time.
"We hugely value our volunteers and many across the country have taken the opportunity to get involved in developing our Prejudice and Pride programme, which explores LGBTQ heritage.
"At Felbrigg, many volunteers have enthusiastically supported a new exhibition, which looks at the life of the extraordinarily generous Robert Ketton-Cremer.
"His decision to leave the house to the Trust was the result in part of the fact that he had never married and had no heirs."
At least 10 of the mansion's volunteers refused to wear the rainbow badges in protest of the Trust's decision to reveal Ketton-Cremer's sexuality.