Pharmacists at Boots, Britain’s largest chain of chemists, have voted overwhelmingly to join a trade union in a long-running dispute about union recognition.

A total of 3,229 Boots pharmacists voted in favour of joining the Pharmacists’ Defence Association (PDA) and allowing it to represent them on issues such as pay, hours and holiday entitlement. This amounted to more than 92% of those who voted.

Only 266 pharmacists (7.6%) supported a proposal for an internal representative committee which was put forward by management as part of a concerted anti-union strategy.

The vote in favour represented 47.5% of pharmacists eligible to vote, passing the 40% threshold necessary before companies are obliged to accept union recognition. Boots said it would respect the vote.

Pharmacists voted last year to stop being represented by the Boots Pharmacists’ Association, a “sweetheart union” which they argued was not independent of the company.

The PDA first sought recognition from Boots seven years ago after alleging that employment terms were being eroded by the company.

Paul Day, the PDA’s national officer, said the votes were a landmark in employment law. “No other employees have ever tried to remove a sweetheart union, even though the law to do so has been in existence for 17 years,” he said.

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The PDA has pledged to improve employment rights and set up a support network for pharmacists experiencing stress and mental health problems. In 2016, the PDA accused Boots of pressuring staff to abuse an NHS scheme intended to help sick patients.

After the result of the ballot, which was announced on Monday night, the union wrote to Seb James, the chief executive of Boots, to reach a recognition agreement and “start a new chapter of employee relations”.

The letter from the PDA general secretary, John Murphy, said: “Boots have expended significant time, effort and money over eight years to try and prevent this group having an independent voice at work, but through the relevant processes, pharmacists have finally had their say and this can no longer be resisted.”

He added: “We now have an opportunity to put all that in the past and create a working environment in which pharmacists feel appropriately valued and respected, patients can consistently receive excellent care and the company can prosper.”

He said both sides had to agree a way to work together. “I am asking you to direct your negotiators to enter those discussions constructively and in the spirit of our joint opportunity to make Boots even better.”

Before the vote Boots argued that it did not want to negotiate with a “third party”. But its pharmacy and retail operations director, Andrew Caplan, said it would now enter negotiations with the union.

“Clearly, this is not the result that we had hoped for, however, we have listened to the voice of our pharmacists and offer our congratulations to the PDAU. We will now enter into a negotiation with the PDAU over the terms of the collective bargaining agreement, how it will work and what it will cover and we’ll continue to keep our pharmacists updated on this process over the coming weeks.”