BBC staff have voted to accept a new pay deal after a hard-fought battle that saw some union representatives threaten to resign in protest at changes to terms and conditions.

Union negotiators struck the deal with the corporation following two years of discussions. As a result BBC will staff benefit from a backdated pay deal under which wages rise by 2% in 2017/18, 2% in 2018/19 and at least 2.5% in 2019/20.

Union leaders say the deal includes an increase in the BBC minimum salary from £15,687 to £20,000 as of August, increased sick pay and wellbeing arrangements, and a simpler, more transparent pay structure.

Messages show that some representatives of the National Union of Journalists at the corporation had raised concerns with union officials about the deal and the way it was agreed. The proposals were agreed earlier this year following all-night negotiations involving management and three unions at the conciliation service ACAS which lasted for 22 hours.

In the lengthy email chains some NUJ representatives threatened to resign if the deal was passed, arguing that union leaders should go back to the negotiating table and demand a more generous package.

NUJ members voted to accept the proposals in a ballot whose results were announced on Tuesday, with 59% in favour and 41% against. Members of the Broadcasting, Entertainment, Communications and Theatre Union – which largely represents production staff – back the deal enthusiastically with 77% support.

During the vote the newsroom in the BBC’s New Broadcasting House headquarters was filled with material lobbying against the agreement. Campaigners against the deal anonymously distributed leaflets arguing that the proposed changes would damage the potential future earnings of young staff joining the corporation and offer less certainty for shift workers. 

The NUJ general secretary, Michelle Stanistreet, welcomed the decision to accept the new deal “It’s now time for the BBC’s commitments to better working conditions and greater work-life balance to be put into action,” she said.

“The new pay structure still requires collective effort to make it work, but it is a structure that will provide greater transparency and assist in holding the BBC to account on pay parity now and in the future.”

Anne Bulford, BBC deputy director-general, said the “simple, fair and consistent proposals” will “benefit staff, the BBC, and most importantly the audiences we serve”.