Boots pharmacists have voted "overwhelmingly" for a new union to have recognition amid concerns they are overworked.
Several pharmacists have previously told the BBC that understaffing could pose a risk to patients.
The Pharmacists' Defence Association (PDA) will now be able to collectively bargain on pay, hours and holidays.
Boots said it was "not the result that we had hoped for" but it had "listened to the voice" of its pharmacists.
The PDA union had been trying to get recognition at Boots for eight years.
In order to finally do this they had to de-recognise a non-independent union called the Boots Pharmacists' Association. This happened following a vote last year.
Mark Pitt, assistant general secretary of the PDA, said: "Boots pharmacists have told us over the years their terms and conditions have gradually been eroded.
"That sort of created a momentum for us to become recognised at Boots.
"It's an overwhelming vote and we are hopeful that will give a clear message to the company that things do need to change and they need to start listening to their pharmacists."
Of the 6,803 pharmacists eligible to vote, 3,229 voted for the PDA to be recognised and 266 voted against. Almost half of those eligible did not vote.
Andrew Caplan, pharmacy and retail operations director for Boots UK, said: "We will now enter into a negotiation with the PDA 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."
About 2,500 Boots pharmacists are members of the PDA union and about 1,200 are members of the Boots Pharmacists' Association.