A Queensland physiotherapist digitally raped a female patient before sexually assaulting another later that day, a court has been told.

Scott Alexander Stuart Mackay, 48, is on trial after two women made complaints following their sessions at a Windsor healthcare clinic, in Brisbane's north, in January 2019.

Both were assaulted on Mackay's massage table during their treatment, crown prosecutor Michelle Parfitt told Brisbane District Court on Monday.

The first woman was attending her second session with Mackay to address knee pain.

Mackay began the treatment by massaging around her knee before working his hands up to her groin, Ms Parfitt said.

He then moved his hand under her shorts and her underwear.

"She felt one or two fingers in her vagina for about one minute ...(the woman) froze when this occurred," Ms Parfitt said.

He moved his hands back down her leg and the treatment soon finished.

The woman later complained to the Office of the Health Ombudsman who referred the matter to Queensland Police.

When interviewed by police Mackay confirmed he was the woman's physio but said the treatment he had provided was "appropriate".

The second woman attended the clinic later that day for her first appointment with Mackay, complaining of back pain.

During her session Mackay moved his hands between her legs and placed his "palm (of hand) on her bottom and fingers across her vagina" for a short period of time, the court heard.

The woman didn't tell anyone until July 2019 when she saw a Queensland Police Facebook post about the first woman's complaint and got in touch with officers.

Mackay has pleaded not guilty to one count each of rape and sexual assault.

The trial continues before Judge Julie Dick.