The 90-year-old attended a Sunday church service at her private Sandringham estate in Norfolk, eastern England, having missed a New Year's Day church service due to an illness that also forced her to delay her Christmas plans.
The world's longest reigning monarch was filmed getting out of a royal car at around 10:55 am (1055 GMT) for the service, accompanied by 95-year-old husband Prince Philip, who was also hit by the bug.
Despite her illness, the queen continued to receive her red boxes containing official papers, and spent Christmas at Sandringham with members of her family, as normal.
However, the royal couple's journey from London to the estate was delayed by a day because of their illnesses.
When she failed to appear on Christmas Day, speculation grew about the queen's health, and a fake report on Twitter that she died prompted news stories in some of the tabloid newspapers.
Fears grew when she missed the traditional New Year's Day service, with Buckingham Palace saying she "does not yet feel ready to attend church as she is still recuperating from a heavy cold."
British newspaper the Daily Mail reported that the monarch had a persistent "hacking cough" and was worried about disturbing other worshippers.
When asked about her mother's health, daughter Princess Anne said she was "better", according to the Daily Mirror.