According to a 1993 Hippon Super magazines interview with the game's producer/scenario writer Hiromichi Tanaka, he was asked what were the biggest things he wanted to accomplish with the development of the game. He responded:

According to game's director and chief designer Koichi Ishii in an Hippon Super magazines interview, his team wanted to add traps in the chests to trick the players so they thought twice before opening them. This idea came from Wizardry series.

Secret of Mana began life on the SNES-CD add-on when Nintendo and Sony tried to form a partnership. However, when the partnership dissolved, a lot of the original content had to be edited out so it would fit on a cartridge.

It is possible for the player to get back into Potos village after they have been banished by walking into the man blocking the entrance with a full party, and then pushing select to change party members. Constantly doing this rapidly will allow the player to walk through the guard.

Hitting the totem poles placed throughout the Upperland forest with the sword will cause them to stick their tongues out. Hitting them again will make them put their tongues away again.

It's possible to explore the Fire Palace without Salamando by using the forward motion of the glove attacks to climb a ramp.

In the NTSC version, there is actually a way to obtain the Mana Sword before the final battle without the use of a cheat device. First, once the Flammie Drum is obtained and the sword is level 8, go to a small isle of the coast north of Ice Country due west of the Ice Palace. Neko will be there. The player should save at Neko, soft reset and start a new adventure. When the player enters the Mantis Ant fight, perform a soft reset once Elliot finishes his lines and reload the save file in Ice Country. Instead of Ice Country, the entire party will be in the Mantis Ant fight. Defeat him and Jema will give the party a Sword Orb. Give this orb to Watts to forge and the player should have the Mana Sword.

When on a screen with your weapon drawn, holding the A and L buttons, and while doing this pressing the R button 39 times, releasing the A and L buttons and pressing R once more will cause the letters "NAS" to appear where the recharge percentage is normally displayed. This is most likely an Easter egg hidden by the Iranian-American programmer, Nasir Gebelli, who worked for Square on the first 3 Final Fantasy titles and Secret of Mana.

In the original Japanese version (Seiken Densetsu 2), the equivalent of the US boss Kettle Kin wields a chainsaw rather than being a carbon copy of its predecessor, Kilroy. What's more, its second form rides around on a giant drill rather than a unicycle.

An NPC on the isle where you find the Sea Hare's Tail claims, "This here island's really a turtle shell!" If you ride flammie above the isle, there is a visible shadow of a head and fins. This turtle may actually be Booskaboo from Seiken Densetsu 3 whom the party travels on before the acquisition of Flammie. Figuring that Seiken Densetsu 3 is a prequel to Secret of Mana, this may hold true.

In Ice Country, a screen south of Santa's House, there is a Howler enemy stuck in the trees, immobile, and only visible when targeted with Lava Wave magic.

There are two unused items in the game's code. The first being a brownish orb which is named "?". Its animation is that of a curing item, but has no visible effects.

The second item is called "Ruby Armet". It is only equippable by Purim (the girl), and offers 46 magic defense and defense. The official Secret of Mana Guidebook still lists it as an available item, even giving it a price and concept art. It also includes this description:

重みを肩で支えることができる構造になっているため,力がなくても動きやすい中量級へルム。また中央にあしらわれた真紅のルビーは,炎のダメ一ジを軽減する効果をもっている。

Which translated says:

This is a midclass helm that does not take energy to move in easily because the structure is such that the weight is supported by the shoulders. Also, with the deep red ruby in its center, it reduces the effectiveness of flame damage attacks.

Due to a miscalculation in the scrolling of the background, the backdrop when you enter the cave to visit Sage Joch differs from the backdrop you see when you exit. The former will still be showing the tops of trees below the mountains, while the latter displays clear blue skies.

In Mandala Temple, there is a group of six orb-like structures. The top-right orb, when examined, makes a reference to the game show Jeopardy!.

It is possible to kill the ferryman, Karon, via targeting him with an attacking spell. The reason for this is because the game recognizes Karon as a Robin Foot enemy whom he shares a sprite with.

The Mystic Book and National Scar enemies, when casting a spell, will land and flip through their pages. However, once in a while, they will "accidentally" flip to a nude centerfold of a naked lady in a seductive pose. The book, embarrassed, will then nervously flip to the right page.

Two faces can be seen on the overworld map as you fly with Flammie. The first is in a rock formation just south of Southtown. The second is off the coast of Ice Country. These are very similar to a natural "face" looking formation on the surface of Mars.