I'm trying to find a circus movie where people were getting transformed into different creatures for a "show" of the circus; one was transformed into some sort of clown/joker, one as a witch and the last one as a beast/werewolf.
Found it. It's R.L. Stine's Monsterville: Cabinet of Souls from 2015.
A small town Halloween festival finds itself intruded upon by an evil carnival with designs upon imprisoning and feeding off the souls of unwary teenagers. Targeted are four high school friends, Kellen, Beth, Nicole and Luke. Beth notices a new kid named Hunter and falls for him. Kellen then meets Lilith (who works at the carnival known as Dr. Hysteria's Hall of Horrors) and starts to fall for her too.
However, Beth notices that Dr. Hysteria's carnival is odd and that her friends have started to act on their more negative traits. This results Luke turning into a clown and Nicole into a witch. Kellen is later led by Lilith to a movie theater hidden in Dr. Hysteria's attraction, which shows the viewer what they dream or desire most; in his case this would be winning Beth's affection from Hunter. This, however, is what Dr. Hysteria uses to capture new victims to use as monsters in his carnival and to feed on their souls as sustenance. Beth is later led to the theater, but is unaffected by what she sees, as she chooses her friends over Hunter; she then learns Hunter and Lilith are Dr. Hysteria's children. They want Beth to join them as her strength is what they seek in family; however, Beth sprays them with a bottle of exorcism materials, paralyzing them. This frees Kellen, their friends and another recent victim. Dr. Hysteria, his children, and his carnival are then sucked through a portal and disappear.
If it was a cartoon and occurred during the 1990's, it matches the description of "Mighty Max" S02E13 (A Clown Without Pity) from 1994:
Freako, who was born with a permanent clown's face, is now out for revenge by capturing kids and turning them into sideshow-like mutants.
I don't remember specifically who got turned into what, but there was definitely a clown and a hairy werewolf-looking creature involved, along with several other generic monster-types.