The parents-of-two, who have almost 1.5 million subscribers on the video platform, shared the heartbreaking news only several hours after finding out themselves.
The video starts with Jonathan explaining; 'Today was a sad day. Anna woke up with some bleeding, we called our consultant and he arranged a scan at the EPU (early pregnancy unit).'
The couple were informed by doctors at the East Surrey hospital that they had experience a miscarriage, after no heartbeat was detected and the amniotic sac was found to be empty.
Although the news has come as a shock for fans, Jonathan explained that the couple, who married in 2012, had been told at a scan a week ago to expect the worst.
More: What are the early signs and symptoms of a miscarriage?
We often take for granted the things that are right in front of us â¤ï¸ I don't give @jonathanjoly nearly enough credit which he deserves ð This man is my best friend & soul mate, the co-creator of my two proudest accomplishments, my business partner, the only one who can cheer me up when I'm feeling down, my personal motivational speaker, the person I rely on when times are tough, the most amazing dad to our babies, the one I still laugh hysterically with, my partner in crime for junk food & movie nights and the saint of a man who doesn't object to my chronic handbag/shoe/dog collecting habit ð¬ðð Love you and appreciate you so much @jonathanjoly ð’ Thank you for being you.
Jonathan explained; 'I like to think everything happens for a reason, I've always lived by this and will continue, thank you all for you support, I tried to make this video as beautiful at the announcement video, and I plan on doing something later on this week to say goodbye.'
The video has sent shockwaves around the YouTube community and has received over 700,000 views in 16 hours.
The Irish vlogging stars have made the decision not to tell their two toddlers, Amelia, three, and Eduardo, two, about the miscarriage, and instead hope to get pregnant again soon and tell the children it was a long pregnancy.
The 28-year-old mother of two had only made the announcement of her pregnancy two weeks ago.
Taking to her Instagram account Anna posted a photo of herself with Amelia, and Eduardo with the caption; 'Surprise #babysacconejoly'
Fans are now using the photo as a place to offer messages of support and condolence to the couple.