The woman's ordeal began at around 10pm on Sunday night when three people entered the Co-op on Broadway in Kirkstall, Leeds.
Two of them then went to the back room of the store and assaulted the woman, causing injuries to her nose.
Another of the trio made a male member of staff, who had been behind the counter, and a male customer go into the back room.
One of the suspects then threatened the woman with a knife, forcing her to open the safe.
The three suspects then took a large quantity of cash and a mobile phone before leaving.
Detective Inspector Charlotte Hails, of Leeds CID, said: "This was a terrifying incident for the staff and they have been left incredibly distressed by the incident.
"I would appeal to anyone who has any information about this incident, or saw anyone in the area acting suspiciously to come forward to the police to assist with our enquiries."
Anyone with any information is asked to contact Leeds CID via 101, quoting crime reference 13170126277.
Information can also be passed to Crimestoppers anonymously on 0800 555 111.