In the Time Bomb mini-quests, each one begins with a random Bomb Gem appearing on the game board. Upon clearing the Bomb Gem, another one falls into the board from above. Bomb Gems also appear after making a random number of matches. The goal of each mini-quest is to remove a specific number of Bomb Gems before their counters reach zero. Depending on the mini-quest, Bomb Gems will count down either after every legal move or by seconds. If a Bomb Gem's counter reaches zero, the mini-quest ends in which the Bomb Gem detonates.
During each Time Bomb mini-quest, Hypercubes fall into the game board every now and then.
- Pausing the game during Time Bomb II and Time Bomb IV causes the gems to vanish, but they reappear upon resuming the game. This most likely happens to prevent "cheating."
- If there is more than one Bomb Gem on the game board, clearing a Bomb Gem does not always cause another one to appear.
- With all Time Bomb mini-quests, the largest number of Bomb Gems that can be on the game board at once is three; extra Bomb Gems will not spawn when that limit is reached.
- In the PC, Mac, Xbox 360, and PlayStation 3 versions; Time Bomb III has a different background than the one featured in the other Time Bomb mini-quests.
- The Chinese Plus version of Bejeweled 3 has two exclusive game modes, Madness Bomb and Rapid Bomb, based on the Time Bomb mini-quests.
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