Hades was originally planned to be the final boss as evidenced by early concept art of the Hill of Despair showing your party facing Hades in the area instead of Necron, but Hades was instead changed to be an optional boss. There are eyes on the face of his sword and on his throne. Blinking disembodied eyes are also seen in the final battle arena, showing the connection between Hades and the original final battle. Incidentally, eyes are also a feature of many Terran structures (e.g. Pandemonium), perhaps implying a deeper connection that was lost or severed in the final cut of the game.

While no exact reason for the change was given, it is believed that Hades ultimately did not fit the theme as an end boss. Hades is based on Greek mythology as a God of death who would have wanted to bring death to everyone. Necron on the other hand is an original entity based on the Greek word for "death" that wanted to bring an end to existence itself.

After finishing the game's end credits, on the "THE END" screen, press R2/L1/R2/R2/Up/X/Right/Circle/Down/Triangle/L2/R1/R2/L1/Square/Square. A menu selection noise should play if this code is entered successfully, upon which you should press Start to be taken to a secret Blackjack minigame. You start with a balance of 1000, and can only bet wagers divisible by 10. If you go bankrupt, you will be sent back to the "THE END" screen, but you can play again by re-entering the code and pressing Start.

Final Fantasy IX is notorious for having one of the worst official strategy guides made for a video game at the time of its release. The reason why was because Squaresoft decided to host essential tips and secrets that players would want to seek out on its PlayOnline website in an effort to promote that, and forced Brady Games to accommodate for the change in the printed guide by directing readers to the website. Brady Games were against the idea because they knew their consumer base would not like it and understood that buying a strategy guide was worthless when the information they needed was online for free. However, they complied because they did not want to lose the exclusivity rights to making a strategy guide for Final Fantasy X. In the end, Squaresoft abandoned this cross-platform strategy guide format following the negative reception from Final Fantasy IX's guide and stuck with printing physical strategy guides for future games.

The updated version of Final Fantasy IX, available on PC, iOS, and Android, included a few additional features:

• High Speed Mode
• Fill HP/MP/Trance
• 9999 Damage Mode
• No Encounters Mode
• Auto-master Abilities
• Auto Lv. 99/Max Magic Stones
• Max Gil
• Cloud storage

In addition to this, character models were updated, and returning to boss fights from the menu was made easier.

Through Square Enix's PlayOnline service, players were able to play an online variant of Tetra Master, the card game from Final Fantasy IX. It used characters from both Final Fantasy IX and Final Fantasy X.

The game was unfortunately discontinued on December 31, 2010.

Inside the weapon shop in Lindblum is a display of large swords. If Zidane inspects the swords, he will comment "I remember a guy with spiky hair who carried something like this." This is a reference to Cloud Strife and his signature Buster Sword from Final Fantasy VII.

Inside the Evil Forest, one of the Active Time Events that can be viewed is "Orchestra In The Forest", which shows the Tantalus orchestra playing a song to boost morale for the crew. The song that they play is actually Rufus's Welcoming Ceremony from Final Fantasy VII.

The character Cinna has a face portrait which goes completely unseen throughout the game. The reason why it goes unseen is because Cinna only ever appears on the player's team for a very brief time, and the player cannot access the submenus to see it like every other playable character.

A secret side-quest was discovered 13 years after the game's release. It involves talking to the Nero brothers a multitude of times while following specific boss battles and story triggers within the final dungeon. The only time this quest was ever outlined was in the Ultimania guide for the game, only released in Japan. There was no reference to the side-quest in the notoriously poor Western strategy guide or the PlayOnline hint website it frequently directed its readers to.

The creature, Ragtime Mouse, is holding a card with an unanswered question on it. The card is in Japanese and reads "Pop Quiz! FF10's theme is GUTS! True or false?" This is the only time that a main Final Fantasy game has alluded to a future Final Fantasy game.

Before you fight the final battle with Spoiler:Necron, he will start monologuing to Zidane about Death and Fear and will say, "Fear leads to anger... Anger leads to hate... Hate leads to suffering...". This is the same quote that Yoda says to Anakin in Star Wars: Episode I: The Phantom Menace.

Before the battle at Cleyra, Beatrix is holding her sword in her right hand while it is still rendered in the sheath on her back.

At the very beginning of the game after fighting the Masked Man, the members of Tantalus meet to discuss their plans to kidnap Princess Garnet. When going over the plan, you will be given a choice to either say you will kidnap Queen Brahne, or kidnap the Princess. If you select the option to kidnap the Queen 64 times, on the 64th time, Ruby will run into the room and say:

In the French, Italian and Spanish versions, Quina is refereed as "she". In the German version, Quina is refereed to as "he". In the American version, Quina is refereed to as "s/he", but the pronouns used are masculine. However, most languages use the masculine pronouns if the gender is unknown.

Freya is the only left handed playable character. This can be in allusion to Kain Highwind from Final Fantasy IV, who is also left handed.

Steiner will not do his victory pose during the party's second visit to Alexandria Castle.

The development team changed the ending seven times before they decided on an ending.

A section of the game can be skipped by obtaining a Gold Chocobo right after getting the Blue Narciss but before getting the airship. This let you bypass The Desert Palace and jump to right before Ispen's Castle on disk 3.

The Downsides:
• Dagger is permanently stuck in her "Mute" condition (no Trance, commands fail on a regular basis)
• The player will have to buy a Ribbon at the Treno Auction House in order to have Eiko learn the Madeen summon, as Mount Gulug will be skipped.
• Ozma will have to be beaten to get a second Pumice Piece to have Dagger learn the Ark summon (since the one in Oeilvert is unattainable).
• Items from the Desert Palace cannot be recovered.

The Upsides:
• Completely skip boss battles such as Ark and Valia Pira.
• Saved time for those who have already played the game, or those trying to obtain Excalibur II.
• Automatic access of Hilda Garde III.
• The Gold Chocobo

This is only possible in early Japanese and North American releases as the items required were made impossible to get at that point in the game in later versions.