The Hive, also known as the Honeycomb, is where the player's bees go to rest when they run out of energy, to convert pollen to honey, or when the player dies. Upon joining a server, the player must first claim a hive by following a red arrow and pressing "E" (on laptop, PC, etc.) or tapping the "claim hive" button (Tablet, iOS, Android, etc.) to claim it. The player must place eggs and royal jellies in hives to use them.
There are 6 hives in a server. A basic hive contains 25 slots for bees. The player can expand their hive by buying additional hive slots at the Mountain Top Shop. The maximum number of bees a hive can contain is 50, but the price of that many hive slots is quite high.
Each bee's hive slot has the face of the bee icon in the bee's color. The background color of the hive slot is based on the bee's rarity; bronze for Common, white for Rare, bright yellow for Epic, aqua blue for Legendary, light purple for Mythic, and green for Event. If a bee is gifted, then a thin yellow glowing line will trace the hive slot border. If a bee is mutated, then the bee's level will turn a different color depending on the mutation.
- A very rare glitch may occur, if the player claims the second to left hive they might be given Onett's Star Journey quest even if they have less than 30 bees.
- Once a player dies, all of their bees return to the hive to rest, but do not recover energy. This is to prevent death abuse. This is known as the death penalty.
- This can be bypassed by resetting 2 times in a row, of which all the player's bees return to the hive and recover energy, and the energy will go back up to maximum. This can be abused if the player's best bee is out of energy. The player will lose all their pollen while doing this glitch though.
- The statue of Onett on the top of the 6th hive has 38217 pollen in his Port-O-Hive, which is a reference to a code with the reward of 5 tickets.
- The 7/11/2018 update introduced a glitch that when looking on another hive, it shows the wrong rarity. This is mostly patched, but still occasionally happens.
- Prior to the 11/25/2018 update, there were only 5 hives in the game.
- In the earlier days of Bee Swarm Simulator, bee faces on hive slots were bigger and they also used to sparkle depending on what rarity the bee was. The rarer the bee, the more sparkles they would've emitted (excluding the Basic Bee hive slot).
- The blue wall next to the leftmost hive wasn't solid after the 4/5/2019 update. Because of this, it was possible to bypass most of the gates without having the required number of bees. This was fixed in the following update.
- According to Onett, this was for a test when he was developing the game. However, he forgot to make the wall solid after testing.