Though unavailable as an item in Pokémon Super Mystery Dungeon, Honey is mentioned as being a food produced by the Beedrill and Combee of Nectar Meadow, overseen by their queen and manager Vespiquen. Due to its nutritious properties, Budew heads to Nectar Meadow to obtain some Honey for her ailing mother, despite being warned that the Pokémon are usually on edge during their Honey-making season. Misunderstood as a Honey thief, Budew is rescued in time by the player and partner from the angry Beedrill and Combee. After they are defeated, Vespiquen intervenes and resolves the misunderstanding, and gifts Budew with some Honey.
In Some Enchanted Sweetening!, Honey was slathered on a tree, attracting several wild Bug-type and Grass-type Pokémon as well Ash's Aipom and Cheryl's Burmy. The Honey appeared to have been slathered by Cheryl, who wanted to catch a male Burmy to help her find the Enchanted Honey. Cheryl later explained to the group that Enchanted Honey was Honey gathered by Combee in the Amber Castle, located deep in Eterna Forest, which is said to be hundreds of times sweeter than normal Honey. With the help of Ash and his friends, and with her Mothim leading the way, she located the hive of a Vespiquen and its many worker Combee. After helping defend the hive from Team Rocket, the Vespiquen shared some of its Enchanted Honey with Cheryl, Ash, his friends, and some of their Pokémon. All of them loved the Enchanted Honey, except for Brock's Croagunk, who looked disgusted by the sweet flavor.
In Honey for Combee, as Diamond, Pearl, and Platinum ventured into Floaroma Meadow, Diamond and his Pokémon smelled Honey and ran off to lick it off a tree, only to be attacked by a swarm of angry Combee, whom the Honey had been meant for. Later, the trio ventured into the Valley Windworks, where they met Mars, who filled the Windworks control room with sand in order to do away with them. Pearl and Platinum ended up outside the building and were able to uncover Diamond's location inside the building and save him thanks to a group of Combee being attracted by the scent of Honey on Diamond and his Pokémon.
The Honey is present in the game data of Pokémon GO, but is unused.
Honey may originally have been planned for Generation II, where unused text refers to an item called Sweet Honey (Japanese: あまいミツSweet Honey).
Regular honey has been seen in various Pokémon canons, even before its official debut in Generation IV:
In A Sappy Ending, certain trees that produce honey-like sap were featured. Like the Honey in the games, this sap was also shown being capable of attracting wild Bug Pokémon, like Heracross, Butterfree, and Pinsir.