In the English version of Lunar 2, there's an Easter egg in place of a glitch seen in the Japanese version. In the first boss fight, if Hiro and Gwyn die at a point that prevents the boss from reaching Lucia, the fight will never end, as the boss cannot kill the last party member. If the same conditions are met in the English version, a cute and tiny character called Ruby that mostly just flies around in the background , will one hit kill the boss.

The files on the disk contain a secret track, in which the game's villain, Zophar, talks about the joys of cheating, and attempts to convince you to become his minion. He mentions that it's evil to rip XA audio files from games.

Though never stated in the game, Zophar's name is short for "Zone Pharaoh", as indicated by the Lunar I & II Official Artbook. This explains the Egyptian motif of the murals seen in the opening credits.