The best place to start the Made in Abyss manga after season 2 is at chapter 38. It ties in well with the end of the season and takes the story in an exciting direction. Just make sure to pay attention to the details as the world-building gets even more elaborate.
I'd suggest starting from volume 7 of the manga. It lines up nicely with what happens after season 2 and continues the adventure smoothly. There are some new plot developments and characters introduced that you won't want to miss.
You can start from chapter 40. That's where the story picks up after the events of season 2.