The game follows the storylines from the original, first three Indiana Jones films: Raiders of the Lost Ark, Temple of Doom and Last Crusade. However, the developers of the game divided the story from the movies into six chapters each in the game, with each a story and a freeplay mode as in the traditional Lego gameplay. The story mode must be played first, restricting the player to use preselected characters, from the real scenes in the movie, in the game, with the option to use any other (unlocked) character during the freeplay mode. These characters can then be used to interact with the environment that other characters sometimes cannot do during story mode to gain new items or find new doorways, puzzles or game collectibles.
Barnett College, Dr. Jones' teaching location from Last Crusade (earlier known as "Marshall College" in the prequels) serves as the main hub of the game, and different maps on the walls allow access to each of the missions, extra unlockable content and options are found in the different classrooms. Once a player chooses a mission, a cutscene begins that introduces the section of the movie being played. Notable scenes have been recreated from the movies, such as the memorable boulder escape and the battle on the rope bridge, or Walter Donovan choosing the incorrect Holy Grail.
There are 82 (standard) playable characters in total, 23 characters which are given to players in the story, and 59 characters which may be purchased from the in-game Library. Then, there are the two custom figures which can be made by the players, and the bonus character Han Solo (much like Indiana Jones was a playable character in Lego Star Wars: The Complete Saga). A few other characters can also be played with the "Secret Characters" extra on, only playable on certain levels (such as Santa Claus in "Into the Mountains" or Dancing girl 2 in "Shanghai Showdown".) Each character featured in the game has his/her own unique ability, which are required to access new areas when replaying a level in Free Play mode. Lego Indiana Jones allows players to mix and match parts to customise characters and make their own creation like "Belloq Jones" or "Colonel Toht".
LEGO Indiana Jones also allows players to customise characters and make their own creation. In addition, players can play as their custom creation in the Art Room to test their character's abilities. However, all custom characters have the Whip ability, which may clash with their custom character's appearance.
New features were added to the gameplay from the Lego Star Wars series, such as the ability for the player to interact with objects in their environment, e.g. bottles, swords and guns. Players can also build and ride vehicles. The game also incorporates character phobias from the films; for example, if Indiana Jones sees a snake, Willie sees a spider or Henry Jones Senior or Elsa see a rat, they will be frozen with fear and have limited movement capacity until the animals are either dead or out of range. Also, new melee attacks, such as the Whip snag (trips enemies), have been added.
