Alongside Anita Rani, Harrison recorded her final episode down in Poole Harbour to mark the end of her 13-year tenure.
Rani had lined up a special seaside meal and a few surprises to bid her co-star farewell.
Harrison was also treated to a number of video messages from the Countryfile crew as they all wished her well for the future.
Matt Baker said from his farm: "Ellie, I'm sending this message with lots of love to say how much I'm going to miss presenting Countryside alongside you and I'll never forget our first show together where you yonked up snow with that freshly harvested mushroom sandwich, much appreciated. See you soon!"
John Craven weighed in to praise Harrison's "warmth", "deep knowledge", and "affection for the countryside" before telling her she'd be a "much-missed" member of the team.
Ellie Harrison was joined by Anita Rani for her farewell
Adam Henson was up next and after telling Harrison it'd been an "absolute joy" working with her, he continued: "I can't believe you're leaving Countryfile after all these years.
"But you've been brilliant to work with, you've brought so much to the programme, particularly your expertise in wildlife."
Several other Countryfile hosts also sent their messages as they paid tribute to Harrison who soon became emotional.
As the pair put the tablet with the video messages away, Rani had a tribute of her own as she told her "heartbroken" co-star: "You're amazing... I am going to miss you a huge amount. You've been amazing to work with."
Before the cameras stopped rolling, Harrison had a short speech of her own in which she thanked her co-stars and the show's audience for over a decade of support.
"I've had the best geography field trips exploring these beautiful lands," Harrison said. "It's been an honour to have been trusted by all the people I've met on the programme and by the audience...
"And I thank you for your time. The programme is still in wonderful safe hands and next week, Matt and Charlotte with be in the Eden Valley."
Harrison and Rani shared a cheers with their seaside cocktails before the episode drew to a close - and fans flocked to social media to share their reactions.
Ellie Harrison heard from several other Countryfile stars via video messages
On X, formerly Twitter, one viewer said: "I am really sorry to see that Ellie Harrison is leaving @BBC #countryfile. Good luck in whatever you do in the future, and I hope we continue to see you on our screens."
A second echoed: "Been watching #Countryfile since it was on at midday with John Craven as main presenter but I enjoyed the Ellie years, very sad she’s leaving. Hopefully going to better things."
"Best wishes to the fabulous Ellie Harrison," added a third. "You'll be greatly missed on countryfile. We hope to see you soon on some other adventure Ellie. #countryfile."
"Best wishes to lovely Ellie. You'll be missed on a Sunday evening #countryfile," a fourth commented while a fifth said: "@BBCCountryfile Devastated that @EllieHarrison__ is leaving after 13yrs [crying emojis], It's been wonderful Ellie. Will miss you."
And some fans even went as far as to vow to stop watching, including one viewer who penned: "#countryfile when Clarkson and co left Top Gear I never watched the downgraded new version. After Ellie goes doubt I will watch Countryfile again."