Her Royal Highness will celebrate through a number of official events in London between the 10th and 12th June 2016 including a thanksgiving service at St Paul's Cathedral, a Birthday Parade on Horse Guards Parade and a street party in The Mall.
The Church wants parishes across the country to host their own celebrations and community events.
It's launched a new website through its ChurchCare initiative to provide tips on how to put on events, how to involve community partners as well as creating publicity opportunities.
Dr John Inge, Bishop of Worcester and lead Bishop for Church Buildings said: "Churches up and down the land will be organising myriad events in thanksgiving for the wonderful Christian service that the Queen has given, celebrating her commitment to God and the common good over ninety years.
"ChurchCare will be doing everything possible to help by offering practical advice and creating a virtual space where communities can share imaginative ideas on how to mark this great milestone in the life of our Queen and nation."
Janet Gough, Director of The Cathedral and Church Buildings (CCB) Division for The Church of England said: "We hope exhibitions, celebratory peals of church bells and festivals will fill our church buildings with people of all generations and from across local communities as they come together to celebrate this important milestone in our national life.
"The ChurchCare hub will be a useful virtual community space and I am excited to see it grow over the coming months."
The Church is encouraging parishes to get in touch to let it know what events are happening across the country.