Ali Harbi Ali, 25, has appeared at Westminster Magistrates Court charged with murdering the MP at a church surgery six days ago.
Sir David tragically died at his constituency surgery in Leigh-on-Sea in Essex - believed to have been stabbed up to 17 times.
Appearing in court today Ali, wearing grey prison-issue clothes with glasses, was flanked by two men in suits during the hearing and only spoke to confirm his identity.
Ali, who was remanded in custody, faces a second allegation, of plotting terrorist acts between May 1, 2019 and September 28 this year.
The CPS today announced the charges, saying that the attack had both "religious and ideological motivations".
Nick Price, Head of the CPS Special Crime and Counter Terrorism Division, said: “The CPS has authorised charges against Ali Harbi Ali for the murder of MP Sir David Amess on Friday 15 October 2021.
"We will submit to the court that this murder has a terrorist connection, namely that it had both religious and ideological motivations.
“He has also been charged with the preparation of terrorist acts. This follows a review of the evidence gathered by the Metropolitan Police in its investigation."
Ali was detained under terrorism legislation.
Assistant Commissioner Matt Jukes added: "I want to send my deepest condolences to the family, friends and colleagues of Sir David Amess, who died so tragically last Friday.
"Sir David’s dedication to his family, his constituents and his community, and his positive impact on the lives of so many has shone through.
"Today's charge is a significant milestone in the case, but the work from my colleagues in the Met's Counter Terrorism Command will continue apace.
"There has been considerable speculation in the media about the background, history and motivation of the man now charged.
"I understand the huge level of public interest in this case, but now a charge has been brought, it is vitally important that everyone exercises restraint when commenting on it publicly, to ensure future court proceedings are not prejudiced in any way."
Sir David's wife Julia and five children paid tribute to the "courageous" husband in a touching statement.
They told how they are "enormously proud" of their husband and father, saying: "Our hearts are shattered."
The statement read: “Strong and courageous is an appropriate way to describe David. He was a patriot and a man of peace."
“So, we ask people to set aside their differences and show kindness and love to all.
"This is the only way forward. Set aside hatred and work towards togetherness.
“Whatever one’s race, religious or political beliefs, be tolerant and try to understand.
“As a family, we are trying to understand why this awful thing has occurred. Nobody should die in that way. Nobody.
“Please let some good come from this tragedy. We are absolutely broken, but we will survive and carry on for the sake of a wonderful and inspiring man.”
On Saturday morning, Boris Johnson joined Sir Keir Starmer and Priti Patel at the church to lay flowers.
Mr Johnson and Sir Keir both wore black suits and carried white blooms as they walked side-by-side to the church during the unannounced visit at 9am.
Mrs Patel, who brought yellow and purple flowers, was dressed in a black coat.
The politicians went to the front of the church individually to pay their respects before returning to their cars, which were escorted by a police convoy.
The PM made his sombre visit hours after describing Sir David as a "much-loved friend and colleague".
"All our hearts are full of shock and sadness today at the loss of Sir David Amess MP, who was killed in his constituency surgery in a church after almost 40 years of continuous service to the people of Essex and the whole of the United Kingdom," Mr Johnson said.
"David was a man who believed passionately in this country and in its future and we have lost today a fine public servant and a much-loved friend and colleague."
Mourners sobbed at a vigil for Sir David over the weekend, with Father Jeffrey Woolnaugh describing the politician as "Mr Southend".
Robert Halfon, Tory MP for Harlow and a friend of Sir David's, called him the “embodiment of Essex man.”
Chancellor Rishi Sunak tweeted: "The worst aspect of violence is its inhumanity. It steals joy from the world and can take from us that which we love the most.
"Today it took a father, a husband, and a respected colleague. All my thoughts and prayers are with Sir David's loved ones."
"He was a good and gentle man, he showed charity and compassion to all, his every word and act were marked by kindness. My heart goes out to his family."
The fatal stabbing comes five years after MP Jo Cox, 41, was gunned down and stabbed to death in broad daylight.
The Labour politician and mother was murdered by Thomas Mair, 53, who was sentenced to life imprisonment with a whole life order.
Her death was the first killing of a sitting British MP after the 1990 death of Conservative MP Ian Gow.
Sir David had written a book last year following Jo's death, saying her murder "spoilt the great British tradition of the people openly meeting" their MPs.
Jo's husband Brendan Cox said: "Attacking our elected representatives is an attack on democracy itself.
"There is no excuse, no justification. It is as cowardly as it gets."
Sir David had served as MP for Southend West since 1997 and first entered parliament in 1983.
Anyone with information or CCTV footage has been asked to call police on 101 quoting incident 445 of 15 October.
Ali left court in an armed police van after appearing to confirm his name
Sir David was married to Julia. The couple had five children together
CCTV caught the alleged killer hours before the murder
Boris Johnson has paid moving tribute to the MP
Police were outside of Ali's home in North London after the attack
Boris visited the scene with Priti Patel and Sir Keir Starmer to lay flowers
His family paid tribute to the 'courageous' MP
Tributes have flooded in for the minister