Frank Zappa's son, Dweezil, along with his Zappa Plays Zappa (ZPZ) band, have featured "Muffin Man" on many concert tours. In 2010, they offered video footage of Frank Zappa playing "Muffin Man," along with isolated Frank Zappa guitar parts, so Dweezil and ZPZ accompanied live Frank Zappa and his extended guitar solo.
The meaning of the song was never fully explained by Frank Zappa, and as such there are many interpretations. The "Muffin Man" of the song appears to be a new kind of food aficionado, one who has taken his love for muffins to a scientific and semi-religious level. He can simply be considered an incarnation of gluttony. More generally, he could represent fanaticism for a certain matter, that turns him away from other interests in life. There are some who have interpreted his loyalty to his favorite food as a parody of the repetitive bourgeois life that Zappa despised. In the chorus an unnamed "girl" is introduced, who appears to have been in a love affair with the muffin man. This part can be interpreted as a record of her sexual delusions: her man was so focused on his research for the perfect muffin that he did not give her pleasure ("no cries is heard in the night" probably refers to orgasms). Considering Zappa's typical sexual themes, it has been speculated that the song can be entirely read as sexual innuendo.