"2 years and still my favorite 😍," she captioned the photo.
Her comments section filled up with messages of congratulations to the happy couple, including a sweet note from Scott himself.
"🥰 I knew two years ago that you were gonna change my life 😘," he wrote.
Jonathan Scott/Instagram Zooey Deschanel and Jonathan Scott
Since getting together, Deschanel and Scott have marked milestones in their relationship for fans to see, celebrating their first New Year together in 2020 with matching Instagram posts.
"A truly Happy New Year with my sweetie! ? ??," Deschanel captioned a photo of herself and Scott, while her boyfriend wrote on his own post, "Once in a lifetime you meet someone who changes everything?"
The couple stayed home together for much of last year during the COVID-19 pandemic, with Scott telling PEOPLE in April 2020 that Deschanel was "the perfect person" to quarantine with.
"I'm blown away, it's really been wonderful," he said, adding, "I think we're just taking it one day at a time here and it's a crazy thing nobody would have predicted. But I'm glad that I'm with somebody that I love, and somebody who's so talented."
While Deschanel and Scott enjoyed their quality time at home last year, the couple has been seizing the opportunity to travel this summer, sharing photos from a trip to San Francisco early last month. Scott shared a peek at the getaway on Instagram, captioning his post, "wonderful adventure to #sanfrancisco this weekend with my ❤️."
He added that he and Deschanel enjoyed "steep romantic strolls and yummy food" on their trip, plus "an excessive amount of escape rooms (3 for 3)."
Deschanel, who currently hosts ABC's The Celebrity Dating Game with Michael Bolton, told PEOPLE last month that she admires her boyfriend's passion and environmental activism, looking back on how the two clicked the very first time they met.
"I remember actually when we first met, he sent me his documentary and I was like, wow, we are so aligned on this level," she said. "Because we both really care about this one issue, but have different areas that we focus on."