The Dog Shrine from the PS4/PSVita version appears abandoned and destroyed when first encountered. A pair of doors in the color of the Switch Joy-Cons have been added to the wall behind the destroyed shrine.
A new boss fight, Mad Mew Mew, was added to the game and can be found in the room behind the Joy-Con colored doors. Accessing the boss immediately is impossible due to the Joy-Con doors, but if you progress far enough in the story and return later, the doors will have crumbled away due to their weak craftsmanship, letting you fight Mad Mew Mew.
A new border was added featuring Mew Mew Kissy Cutie, unlocked by doing the Mad Mew Mew fight. It is titled either "Real" or "Not Real", depending on how the player answers Undyne's question of whether or not anime is real.
Clam Girl's dialogue was modified again, this time hinting at a possible future meet with "Suzy", and she was given an alternate gray sprite akin to the Gaster Followers.
Protagonist can find the fifth Froggit in a long hall north of the Spider Bakesale.