There are two main components to Jewels of the Amazon: a Quest mode and a Blitz tournament mode. Quest mode sees players working their way through a series of levels to follow a story revolving around the hunt for lost relics. Levels are completed by meeting various score targets to win stars; at least one star is required to progress to the next level, otherwise a life is lost.

Blitz mode, meanwhile, is exactly what veterans of Bejeweled Blitz will expect: players are given a minute in which to score as many points as possible, and are then ranked on a weekly tournament leaderboard against other friends playing Jewels of the Amazon. Blitz mode does not require lives to play, but only allows certain rewards to be earned once per week.

Gameplay is fundamentally identical to PopCap's Bejeweled and its numerous imitators. Players swap pairs of gems on a grid in order to match three or more in horizontal or vertical lines. Matching four or more at once produces special gems which may blow up a 3×3 area, destroy all gems in the same row and column or destroy all gems of the same color. In both modes, powerups may be purchased to make things easier — some cost Facebook Credits, while others cost the game’s soft currency, earned through play.