Merlee returns in The Flip Flop Show. In this show, she lives in a mansion at Gloam Valley. She later moves to Flopside in a building adjacent to Dyllis's house in Flipside to help Bleu and his party. This Merlee appears rather angular and strange (not looking even vaguely like past Merlees), taking on the appearance of other female members of Merlon's clan. Like the Merlee in Paper Mario: The Thousand Year Door, this may be a different Merlee. It also could be the same Merlee from Paper Mario because she wants her crystal ball back from Dyllis, and Dyllis borrowed Merlee's Crystal Ball in Paper Mario.

Merlee's Mansion is a major place in Chapter Two. Winnie also makes an appearance here, initially posing as Merlee's maid in her standard form, then eventually Merlee herself – in three separate occasions, in fact. The first is when she attempts to trick Bleu into thinking he finally found Merlee, but an apparition of the real Merlee appears, exposing her as a fake. She impersonates Merlee again once the real Merlee is found, causing a confusion that is only settled with a game show hosted by The InterNed. During the subsequent battle with Winnie, Merlee cheers from outside the bathroom, healing Bleu and his party. After Winnie is defeated, Merlee gives Bleu and his party the third Pure Heart. Much later in the game, Winnie disguises herself as Merlee once more in Castle Pook, asking Bleu and friends what monsters they fear the most.

This Merlee is Dyllis's rival, and has been ever since they were classmates. After Chapter 2, Merlee works as a fortune teller in Flopside. She begins a trading sequence by requesting that Bleu bring her a Crystal Ball from Dyllis. Merlee also apparently once helped Dyllis greatly sometime before the events of The Flip Flop Show, as Dyllis tells Bleu and friends to tell Merlee "Now we're even" as they give her the Crystal Ball. In the end, Merlee gives Bleu a key that unlocks the building holding Sipsi.

Merlee's charms work differently in this show than the previous games. For her cheapest spell, she'll make Bleu get a helpful item every time he kills 25 enemies for 10 times. For the medium priced, she'll give Bleu a helpful item every time he kills 20 enemies for 15 times. And for the most expensive, she'll give Bleu a helpful item every time he kills 15 enemies for 25 times. She is very useful for the Pit of 100 trials. She will, however, allow the Bleu to receive all levels of charms for free if Bleu brought her the Crystal Ball from Dyllis.

Official art of Merlee.