She and the Duke of Edinburgh fell ill days before Christmas, forcing her to delay her trip to the Norfolk estate and to miss a Christmas Day ceremony at St Mary Magdalene church.
Buckingham Palace said the Queen was still suffering the effects of the cold and had decided not to attend the service with other members of the royal family.
A Palace spokeswoman said: "Her Majesty The Queen will not attend Sunday worship at Sandringham. The Queen does not yet feel ready to attend church as she is still recuperating from a heavy cold."
But Prince Philip, who has recovered from his own cold, was well enough to attend the ceremony, led by the Bishop of Norwich, with other members of the royal family.