Some had queued from the early hours of the morning in the hope of seeing the Royal Family.
Well-wishers hampered out flowers and endows for Princess Charlotte, four, and Prince George, six, who were accompanied by their parents, the Duke and Duchess of Cambridge.
There had been surmise over whether Prince Andrew would join the rest of his family at Sandringham, after controversy over his links with billionaire sex offender Jeffery Epstein appreciated him sidelined from royal duties.
While most of the family arrived in front of gatherings lining the roads, Andrew, accompanied by his brother, arrived earlier at the church and used a different entrance.
His daughters, Princess Beatrice and Princess Eugenie, both attended the main service.
The BBC’s royal correspondent Nicholas Witchell said the prince was a “significant absentee” from the prime service at 11 am.
Our reporter said: “If he had attended[ the prime busines] a lot of the coverage would have been around him. He has become … something of an discomfort currently to the Royal Family.”
The Queen’s attendance at church predated her Christmas Day message – in which she described 2019 as “quite bumpy”.
She said that “positive things” could be achieved when gaps were set aside and beings came together “in the spirit of friendship and reconciliation”.
“As we all look forward to the start of a brand-new decade, it’s worth remembering that it is often the small steps , not the monstrous changes, that bring about the most lasting change, ” she said.