The siblings attended the Westminster Abbey service with their respective husbands, Edoardo Mapelli Mozzi and Jack Brooksbank, and were visibly emotional throughout.
WATCH: Beatrice and Eugenie look after mum Sarah Ferguson at the Queen's funeral
However, royal fans were quick to express their confusion after both Beatrice and Eugenie appeared to leave the funeral service early.
They were sat in the second row of the Abbey, on opposite sides of the aisle. As the service started to come to a close, the sisters were seen getting up and seemingly making their way out of the Abbey together.
Their mother, Sarah Ferguson, also looked poised to get up and leave with them but ultimately decided to remain in her seat.
Viewers took to Twitter to express their surprise. "Where did Beatrice and Eugenie just go?" one enquired, while a second added: "What happened with Beatrice and Eugenie? They left their seats and held up the bearer party… even Sarah was going to get up and leave. Strange."
But both Beatrice and Eugenie were seen with the rest of the royal family as they congregated outside the Abbey at the end of the funeral.
It comes after the sister issued a joint statement at the weekend in honour of their late grandmother.
It read: "Our dearest Grannie, We've not been able to put much into words since you left us all.
"There have been tears and laughter, silences and chatter, hugs and loneliness, and a collective loss for you, our beloved Queen and our beloved Grannie.
"We, like many, thought you'd be here forever. And we all miss you terribly."
They continued: "You were our matriarch, our guide, our loving hand on our backs leading us through this world. You taught us so much and we will cherish those lessons and memories forever.
"For now dear Grannie, all we want to say is thank you. Thank you for making us laugh, for including us, for picking heather and raspberries, for marching soldiers, for our teas, for comfort, for joy. You, being you, will never know the impact you have had on our family and so many people around the world.
"The world mourns you and the tributes would really make you smile. They are all too true of the remarkable leader you are."
The emotional statement concluded: "We're so happy you're back with Grandpa. Goodbye dear Grannie, it has been the honour of our lives to have been your granddaughters and we're so very proud of you.
"We know that dear Uncle Charles, the King, will continue to lead in your example as he too has dedicated his life to service. God save the King. With our love, Beatrice and Eugenie."
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