Season 3 was the last season aired on GMA Network, it aired it at an earlier time of 8:25am, still on Sundays as a result of the carrying the Chinese live-action show "Blazing Teens" at 8:50am and the network produced program "AHA!" aired at 9:15am. Starting from this season until season 6, "Jollitown Theme Song" is used on the opening sequence, as well as the songs for the show were now produced by Hit Productions. It is aired as part of GMA Network's 60th anniversary year. This is the only season of the show to premiered in August with the finale aired in the holiday season, and it is also the last season to be oversight by the team at GMA Marketing and Productions, Inc., along with Jose Abacan which is also served as the executive in charge of production for GMA Network until season 6, but it is also mark the network's entertainment head Willma Galvante's final season as the network's executive in charge of production, all in their respective uncredited roles.
Mr. Q. Rakot (Apollo Abraham) and Asiong (Aldel Ramos) visit Jollitown, but a group of henchmen want to destroy the trees to create a new building.
Nana and Mindy celebrate Fiona's birthday, but her mom insists on getting only simple things.
Nikki's mom (Bianca Rafael) accompanies Jollibee and his friends to help Nikki (Jaja Borja) on her first day of school.
Mark (Alec Montemayor) is a boy who lives with his grandfather (Chinggoy Alonzo) and prefers to stay alone. Jollibee and his friends help him find friends.
The Jollifriends join the choir competition, and Mr. Pilot (Alec Humprhries) and Lady Diva (Yassi Pressman) come to Jollitown to support.
Moe (John Claude Yambo) tries to visit the Jollitown Science Fair, but instead they meets the aliens named Crom, Quick and Quack.
Tim (Basty Alcanes) tells the children need to bring back things they have borrowed.
A group of people in Jollitown try to stop Wally from crying.
Jet prefers to play the Doctor Destructo video game instead of going outside. However, Doctor Destructo comes to life and tries to destroy Jollitown.
Sarah (Maxine Rivera) asks Jollibee and his friends to remove her tooth, but the Tooth Fairy (Rebecca Bote) makes the tooth again.
Nolan (Nathaniel Britt) try new things while playing games, but Mr. Q (Apollo Abraham) and Asiong (Aldel Ramos) reveal a new invention in the sky.
Mang Johnny (Neil Sese) wants to cheer for his daughter Danielle (Gianne Cutler) in a "Show and Tell" in Jollitown.
The superhero Afredus Augustus (Paolo Contis) battles against Sinistro (Epi Quizon) to save the statue in Jollitown, but Alfredus accidentally zaps Jollibee, causing him to disappear. Could Jollibee's friends save him from Afredus Augustus?