- Classic is the standard gameplay mode from previous installments of the game, which involves attempting to score as many points as possible before no more moves are possible. Filling up the progress bar advances the player to the next level, where the player receives more points, but requires more points to proceed to the next.
- Zen is an endless variation of the Classic game mode, where the player cannot run out of moves. New gameplay elements to this mode include a unique theme and soundtrack, and Zen Options, which enable several player soothing options such as a breathing indicators and sounds, subliminal messages that display on the game board and progress bar, ambient sounds and binaural beats which uses a wide variety of aural tones emitted from headphones to trick the human brain into hearing different sound frequencies.
- Lightning is the game's timed mode, which involves attempting to score as many points as possible within the time limit of one minute. Matching Time Gems adds extra time to the Time Extension tank, which activates and replenishes up to one minute of time once time runs out, in which the current score multiplier is also increased. The game mode also features the "Speed Bonus" and "Blazing Speed" bonus from Bejeweled Blitz, which activates if the player makes consecutive matches at a rapid pace. In the HTML5 version of the game, the game mode is referred as Speed.
- Quest involves completing 40 different mini-games known as "quests" to restore five Lost Relics of Bejeweled, which have been darkened over time. The quests vary in gameplay, such as rescuing butterfly gems, digging for gold, battling ice storms, uncovering buried treasure and more.
- Poker is a secret game mode, which is also an endless variation of the Poker mini-quest from Quest. The game mode involves attempting to make as many high scoring hands as possible before they land on a skull-marked hand. Matching a gem adds that gem's color to one of five hands. When all five hands are filled with gems, the hand is evaluated, and points are awarded depending on the hand they achieved.
- Butterflies is a secret game mode, which is also an endless variation of the Butterflies mini-quest from Quest. The game mode involves attempting to match butterfly gems, which generate from the bottom of the board by matching and detonating them with Special Gems before they reach the Spider Gem on the top of the board. It is unlocked by reaching level 5 in Zen.
- Ice Storm is a secret game mode, which is also an endless variation of the Ice Storm mini-quest from Quest. The game mode involves attempting to destroy rising ice columns by matching gems on the ice columns they overlay. Making horizontal matches will push the columns down, while making vertical matches destroy the columns. Lowering/destroying ice columns fills up a water tank, which increases the current score multiplier and pushes down all ice columns when filled. If an ice column reaches the top of the board, a skull will appear on the top of the column, and an "internal" ice column begins to rise on the inside, which ends the game if it reaches the top and is not lowered after a few seconds, which causes the game board to freeze. Lowering an ice column eliminates the internal ice column. The game mode is unlocked by scoring 100,000 points in Lightning.
- Diamond Mine is a secret game mode, which is also an endless variation of the Gold Mine mini-quest from Quest. The game mode involves attempting to dig out as much treasure as possible before time runs out. Matching gems next to dirt removes the dirt, allowing space for more gems to fall down. When all dirt is dug above the white line, the game board begins moving deeper into the earth, bringing back dirt up to the game board, but also adding extra time (30 seconds in most versions, 25 seconds in Bejeweled Classic). Clearing all dirt off the board at once awards the player with a large amount of time (90 seconds normally, 75 in Bejeweled Classic). Rocks require extra matches to dig completely, while Dark Rocks, which are found later in the game, can only be destroyed by the detonation of Special Gems. Treasure acts as the point system in this game mode. It consists of gold, diamonds and artifacts. Deeper levels of depth feature more valuable treasure, which award a large amount of points. This mode is unlocked when four quests in Quest mode are completed.
- The Time Bomb modes (Time Bomb and Match Bomb) are two game modes that appear exclusively in the Chinese re-release of Bejeweled 3. They are both endless variations of the Time Bomb mini-quests from Quest, and are available from the start. The game modes involve attempting to destroy the randomly generating Bomb Gems from the board before their counters reach 0. The counts on the bombs decrease every move in Match Bomb, while it decreases every second in Time Bomb. If a Bomb Gem reaches 0, it explodes and ends the game.