The original MSX2 release was soon followed by a version for the Famicom Disk System (published by Tokuma Shoten) called Puyo Puyo Disk Drive. A cartridge version for the Famicom would be released by Tokuma Shoten later in 1993. All of these versions are mostly one-player games with an Endless mode and mission modes, in which the player must eliminate all Puyos from the game field by using limited pieces, although the Famicom version includes a 2-player competitive mode.

A year after the MSX2 version, Sega released an arcade version, which heavily expanded the previous versions by including a one-player story mode and a competitive mode. Ports from the arcade version have been released for many different systems, including Super Famicom, Sega Mega Drive, PC-Engine, Game Gear and Game Boy. However, most of these ports were only released in Japan. The Mega Drive version was a bestseller in Japan for 4 months. The Sega Mega Drive version was re-released for the Wii Virtual Console in Japan on December 2, 2006, while the arcade version was released for the Japanese Virtual Console on April 12, 2011. The arcade VC release features online play. The American version for the Mega Drive on the Virtual Console will be released soon.

Before being branded as Puyo Pop internationally, the first game saw release outside Japan in 1993 as Dr. Robotnik's Mean Bean Machine for the Sega Mega Drive, Game Gear, and Master System (The SMS version was released in Europe and Brazil), and two years later as Kirby's Ghost Trap (European Super NES version) and Kirby's Avalanche (North American Super NES version).

The game was also ported to Amiga by request of Amiga Power magazine and was featured on a cover disk under the name Super Foul Egg. It was then ported to RISC OS on Acorn by Owain Cole (and featured on an Acorn User cover disk), and finally ported to Java. In late 1995 it was ported to the Apple IIGS by Bret Victor.

An English-translated version of the arcade game was released in Europe. This version adds English voice work, changes many of the characters' names, and removes Harpy's (now "Dark Elf's") wings. Additionally, the Game Gear port of Puyo Puyo contains an English version named Puzlow Kids; this version appears whenever the game cartridge is used in a North American or European system. Both English releases use the same ending text, but Puzlow Kids renames the eponymous Puyo to "P-Kids."

The N-Gage version of Puyo Puyo stories becomes different, however. The character's colour is different than the original. The stories about Arle save the world from Satan's grasp turn into a little girl (Arle's counterpart) that lost her way home. The characters are nameless and some opponents in some stages are replaced (though Schezo, Minotaurus, and Rulue don't appear in the N-gage version, they're replaced by the stronger version of Sukiyapodes and Harpy with different colours).

The main game of Puyo Puyo is played against at least one opponent, computer or human. The game itself has three modes, Single Puyo Puyo, Double Puyo Puyo, and Endless Puyo Puyo.

Double Puyo Puyo

In this mode, two players play against each other. In exactly the same fashion as before, by out-chaining one another, the player tries to fill up their opponent's grid. Since the rules of sending so many garbage blocks made games short-lived, no matter how many chains are sent, Compile added the rule of Sousai in Puyo Puyo TSU and onwards. This enables players to counter opponents' attacks with chains of their own, sending any garbage blocks back to them as a result of overflow.

Single Puyo Puyo

In this game, the player takes on the role of Arle Nadja, a 16 year old female spellcaster that has the pleasure of foiling Satan's plans. Satan wishes to take over the world, and Arle stands in his way. Arle must first however battle her way through 12 opponents before facing Satan, and unlike Dr Robotnik's Mean Bean Machine, with the exception of Rulue, they are not under Satan's control, nor were they created by him (for Rulue, she fell in love with him). Once Arle has beaten Satan, the world is saved, so she can return home.

As in all main Puyo games, the story mode consists of playing Puyo matches against a fixed sequence of characters in one of three courses. The characters faced are listed below.

Arle Nadja (アルル・ナジャ, Aruru Naja)

The heroine to the series; she loves Carbuncle/Kaa-kun (her pet) more than anything. She is also a sorceress, and can manipulate fire, ice, and lightning among other things. During chains, she yells "Fire", "Ice Storm", "Diacute", and "Bayoeen", all of which were spells available to her in the Madou Monogatari series. Renamed "Silvana" in the European arcade version.

Carbuncle (カーバンクル, Kābankuru)

Arle's beloved pet, one Satan tries to steal away from her. A fun-loving, curry-eating, bunny-like creature that turns out to be one of the strongest players of Puyo Puyo later in the series. He is more of a helper in Puyo Puyo. He is called Has-Bean in Mean Bean Machine.

Beginner levels

Skeleton T (スケルトン-T, Sukeruton Tĩ)

A skeleton that takes a liking to herbal tea (He sometimes calls it a potion which will make him virtually invincible.) His skills are among the weakest, and is usually one of the first opponents that you face. Has a bit of a temper. Known as "Skeleton" in the European arcade version.

Nasu Grave (ナスグレイブ, Nasu Gureibu, lit. "Eggplant Grave")

An eggplant who wears square glasses. He mainly bounces up and down, as his stubby legs cannot run that fast. Likes to call people "eggheads". Known as "Blue Ghost" in the European arcade version.

Mummy (マミー, Mamī)

An Egyptian mummy who seems to be over-wrapped in bandages. He tries to control greater power.

Normal levels

Draco Centauros (ドラコケンタウロス, Dorako Kentaurosu)

A female human-dragon hybrid who wishes to be the greatest rival to Arle, not just in Puyo Puyo. She, like a dragon, possesses the ability to breathe fire (shown in Puyo Puyo Sun). She has quite a fiery temper, and aggressively challenges other girls to beauty contests. Renamed "Dragon Woman" in the European arcade version.

Suketoudara (すけとうだら, Suketoudara, lit. "Alaska Pollock")

A large fish with muscular arms and legs. He is very proud of these and tries to use them in any way he can. For some reason, whenever he's around, nearby people begin to crave fish. Named "Goby Captain" in the European arcade version.

Sukiyapodes (スキヤポデス, Sukiyapodesu)

A fierce sciapod with a baby face. Renamed "Small Foot" in the European arcade version.

Normal & Difficult levels

Harpy (ハーピー, Hāpī)

An angel creature who sings off-tune, high-pitched songs. She is renamed "Dark Elf" in the European arcade version, and additionally has the wings removed from her sprites.

Sasoriman (さそりまん, Sasoriman, lit. "Scorpion Man")

A guard dressed like a scorpion. He is usually happy, except when he is defeated. Goes by the literal translation of his name (Scorpion Man) in the European arcade version.

Panotty (パノッティ, Panotti)

A sprite who plays panpipes. He likes to see people dancing to his music. Renamed "Johnny" in the European arcade version.

Zombie (ゾンビ, Zonbi)

A zombie which looks like he was put together with spare parts.

Witch (ウィッチ, Witchi)

A witch dressed from head to toe in blue. She also gets the giggles at random moments, and she has the ability to summon comets.

Zo-Daimaoh (ぞう大魔王, Zō Daimaō, lit. "Elephant Great Demon King")

An Indian elephant with a mighty strength. He's provoked easily, as if insulted. Named "Elephant Lord" in the European arcade game.

Schezo Wegey (シェゾ・ウィグィィ, Shezo Wigwyi)

A 180 year-old swordsman who longs for Arle's magic powers, though that lust for power is mistaken as a lust for Arle herself. Renamed "Devious" in the European arcade version.

Minotauros (ミノタウロス, Minotaurosu)

Rulue's bodyguard. He is a humanoid bull with a scar over one eye. Renamed "Max Minotaur" in the European arcade version.

Rulue (ルルー, Rurū)

A skilled martial artist that has a liking to Satan, and will do pretty much anything he says. She is jealous of Satan's obsession with Arle. Renamed "Lulu" in the European arcade version.

Satan (サタン, Satan)

The comical villain of the Puyo Puyo series. He, like Draco, has dragon horns and cape wings. He wants to make Arle his fiance and reclaim his former pet Carbuncle. He is known as "Dark Prince" in all English releases, including the unreleased Puzlow Kids translation.

• Puyolin