It was revealed on Wednesday that Aston Martin is to become Honda's official works partner in 2026, having previously announced its exit from F1 in 2021.
The Japanese manufacturer formally quit F1 that year but has continued to support Red Bull's engine division.
Its future beyond the end of 2025 when its Red Bull deal ends had been unclear, with the Milton Keynes-based team working with Ford for its own Powertrains efforts from 2026.
Honda says its decision to commit to F1 so soon after walking away was triggered by the series' commitment to increased sustainability ambitions.
Speaking ahead of this weekend's Monaco Grand Prix, Verstappen said it was "a bit unfortunate how all of that turned out," referring to Honda's U-turn.
He said he had "loved working with [Honda]," adding that "for Aston Martin, it's really good."
Verstappen said: "I think from our side, of course, it's a bit unfortunate how all of that turned out because a few years ago, they say we're gonna stop, so then Red Bull sets up its own engine division, and then at one point they say no, we continue.
"Unfortunately, once you're already in the process of building a whole engine yourself, you can't really work together anymore. It's a bit of a shame, I would say.
"We always have and had a really good relationship with them, and then seeing them go to Aston Martin is a bit of a shame.
"But I mean, we are also very excited from our side from 2026 onwards to see what's going to happen together with Ford.
"It is what it is. A few years ago, we thought they were gonna leave, (but) now they stay and they go with Aston Martin.
"For Aston Martin, it's really good, they have a great engine, we all know that. So it is what it is."
He added: "I love working with them, we've had a lot of success already, so of course I will be sad to see them go at one point, but we already expected that right?
"Because they said we're gonna pull out, so we already had a kind of a goodbye. But yeah, it is what it is.
"I mean, of course, I'm happy for the Honda people that they stay in Formula 1, but sad to see them go."
Additional reporting by Ronald Vording
