Bejeweled 3 returns to the traditional match three formula after the slightly different spin off Bejeweled Twist. As in previous games, the player is presented with a board filled with gems of different colours. The aim of the game is to remove gems from the board by swapping adjacent gems so that a chain of three or more gems is created. New gems will then be generated at the top of the screen and fall down in the empty spaces. This can lead to a chain reaction when gems fall down and create new matches. New in Bejeweled 3 is that the player can continue swapping gems during a chain reaction. There are some special gems; flame gems are created from a match of four gems and explode when matched, thereby removing surrounding gems. A match of five gems will create a hypercube which can be matched with any adjacent gem and then destroy all gems of that colour. Star gems are created by T- or L-shaped matches and destroy all gems that are right, left, up and down of the it.

The game has four game modes: classic, zen, lightning, and quest. Classic is the original concept known from previous games. It is untimed and ends when no further moves are possible. The zen mode is meant for relaxation and has no end. Here the player can turn on various audio-visual effects. These are breath modulation, ambient sounds, mantras and binaural beats. Lightning is a timed mode and ends when the time is out. The standard time is one minute but by matching special time gems more time is added. The quest mode consists of a number of challenges. The player has to activate relics and each challenge corresponds to a relic.

There are also four additional secret modes that are extended versions of quest mode challenges. These are poker, butterflies, ice storm, and diamond mine. In poker mode, the player has to make poker hands with gem matches. For example, two of a gem type is a pair. The butterflies mode has special butterfly gems that move up from the bottom. These have to be matched before they reach the top. In the ice storm mode, ice moves up the board and the player has to make matches to knock it down again. In the diamond mine mode the lower part of the playing field is filled with rocks. The player has to dig through it by matching gems that are adjacent to it. By doing so gold coins, artifacts and diamonds can be mined from the rock.

The browser version is made using HTML5 and runs through Google's Native Client. Unlike the original 2000 browser version that served as a trial for the full Windows Bejeweled game, this is a complete release made available for free. There are two graphics modes, for faster and slower machines. It has only two game modes however, classic and speed (the latter identical to lightning), with the same power-ups.