Season 5 was the final season of Jollitown to be broadcast on ABS-CBN. The previous season's time slot of Sunday, 9:00am was kept. This season introduced new supporting characters, including the antagonists Virus Elvira (Jolly Lupisan Yu) and Robin No Good (Dene Jennel Gomez), along with the Elders (Ildelfonso Adao and Antonette Maningo). With the kids now reduced to just two, the focus shifted to exploring landmarks and embarking on a quest to find crystals. It is the only season of the series to be presented as part of ABS-CBN's "Bida Best Kid" children's programming advocacy campaign, and the final season to be overseen by ABS-CBN's Corporate Communications Managment (CCM) team and Cory Vidanes, who also serves as executive in charge of production for the network.
Jollibee and his friends are appointed by the Council of Values to retrieve the stolen Crystals of Values from Virus Elvira and Robin No Good, who have scattered the crystals across landmarks in the Philippines.
Jollibee and his friends meet Emilio Aguinaldo and find the first crystal in his house. Note: Staring from this episode, the first minute of the previous episode has cut to Jollibee saying "Sumama din kayo sa bagong natin adventures!" during the opening sequence, this is used until episode 13.
Jollibee and his friends are travel to Vigan with a little help from Lolo Pearl (Nelson Cruz) in order to find the second crystal in the Bangui Windmills.
Jollibee and his friends welcome Diego (Cesar Cruz, Jr.) to the team in a trip to Laguna in order to find the third crystal which is located on a tree.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), travel to Bacolod City to find the fourth crystal, watching the MassKara Festival performance by a group of dancers (Bunganda Dancers).
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), visit Palawan in order to plant trees and to find the fifth crystal in the ocean with the help of Bing (Alyah Marie Valentin) and Palikpik (Miles Jerome Borabon).
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), learn about honesty in a trip to Batanes.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), find the sixth crystal within the ruins in Batanes.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), head out to Davao in order to find the seventh crystal.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), visit Ifugao to find the eighth crystal.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), travel to Cebu City to play music and find the ninth crystal.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), travel to Manila to get the final crystal, but Virus Elvira tries to foil their plan.
Jollibee and his friends, along with Diego (Cesar Cruz, Jr.), confront Virus Elvira and Robin No Good to restore the crystals and bring back order to the Council of Values. Note: Last episode to be broadcast on ABS-CBN, the network later cancelled the show in February 2013, the show was later revived by GMA Network in June 2013.