Prince Andrew also lives on-site at the lodge and is understood to have been at home each time.
In the latest incident, police found the intruders in the lodge grounds and the pair were arrested and taken to Maidenhead police station. They were later released on police bail pending further inquiries.
In the previous incident, a woman aged 44, turned up at a lodge gate in a taxi claiming to be Andrew's fiancee, stating the pair had a lunch appointment.
Guards allowed her in and she spent more than 20 minutes walking around before going into the lodge where she was finally stopped in the lobby.
She was later arrested on suspicion of burglary but was later sectioned under the Mental Health Act.
The grieving Queen, who lives nearby at Windsor Castle, has spent more time at the lodge since the death of husband Philip.
Speaking to the Sun, Ken Wharfe, Princess Diana's personal protection officer for seven years, said Saturday: "When you take these incidents into account then it is a farce.
"It is totally unacceptable and makes the Queen vulnerable. This is very worrying and things really need to change."
A source told The Sun: "This is an astonishing lapse. Everyone was on high alert after the first intruder, now this happens. Heads could roll. It is unforgivable.
"The couple wandered around for ages before anyone spotted them and police were called.
"Andrew was at home at the time. You have to wonder what on earth is going on up there."
The incidents raise questions over whether the Queen would be better off at Buckingham Palace.
But royal biographer Penny Junor said Her Majesty prefers staying at Windsor.
She said: "No one would wish to deprive the Queen of seeking solace wherever she chooses but it is worrying that security should be so lax around a building where she is such a frequent visitor.
"Andrew was in. By the grace of God, the Queen wasn't. But she might well have been.
"She has been spending increasing amounts of time with Andrew since the Duke's death.
"Today security at Buckingham Palace is state-of-the-art — and possibly the only royal residence that is."
The Queen has spent the past seven months at the castle because of Covid-19 restrictions.