In the Japanese release of the game, Klavier Gavin is portrayed as a J-rocker archetype, and as such peppers his speech with random English words and phrases "as a way to elevate his coolness factor". As such, series localization director Janet Hsu felt they needed to make Klavier "sound cool with a hint of foreignness in the English version". It was decided his J-rocker persona would be localized into English as a German rockstar, figuring that he was perhaps inspired by fellow German bands such as Rammstein and Tokio Hotel, who were popular in the late 1990s and early 2000s.

Apollo Justice's first name was chosen as a way to rival Phoenix Wright's. Being named after the mythical Greek bird with a powerful presence, the team decided that Apollo's name had to be something equally as powerful, choosing the Greek god associated with the sun and prophesizing the truth. Other names that were considered were Arthur, relating to King Arthur, and Justin, which phonetically sounds like "Justice". Similarly, his last name "Justice" was chosen to contrast "Wright"; according to product marketing manager Colin Ferris: "Where Phoenix always fought for your rights, Apollo fights for Justice!" "Justice" was actually among the top picks for last names, but two of the other names that were considered were Swift (inspired by the phoenix and to imply "swift justice") and Startel, as a parallel of his Japanese last name, Odoroki, which phonetically sounds the same as the word for "surprise". The motif of naming the main playable character after Greek mythology was continued in subsequent games with Apollo's colleague, Athena Cykes.

The limited edition of the Japanese version of Apollo Justice: Ace Attorney came bundled with Gyakuten Saiban Jiten, an interactive encyclopedia that allows players to read about the contents of the first three games, view character sprites, and play music from the games. When asked in 2009 if it would ever be localized in languages in other than Japanese, series product marketing manager Colin Ferris stated that they were looking into ways to bring it to North America, but these plans never came to fruition.

Shu Takumi originally wanted the Ace Attorney series to end with Phoenix Wright: Ace Attorney - Trials and Tribulations, as he felt that main character Phoenix Wright had been fully explored and had no reason to continue, stating:


When it was decided that a fourth game would be made, Takumi wanted the game to have a new main character and story, with Phoenix originally not planned to appear. However, his colleagues wanted Phoenix in the game in some form, which ultimately led to him being the defendant in the game's first case, "Turnabout Trump".

According to series creator Shu Takumi in a 2017 interview, Capcom executives issued two mandates affecting the writing of Apollo Justice: Ace Attorney. The first mandate was that the game had to include Phoenix Wright in the story, which went against his original idea for a soft reset of the series. The second mandate was to incorporate the Lay Judge system, a real-life judicial system, into the story, resulting in the creation of Spoiler:the MASON System game program and the trial run of a new Jurist System in the game's last case "Turnabout Succession". The motivation for the second mandate is believed to stem from real-life changes in the Japanese legal system happening at the time of the game's release. While Japan previously suspended an older jurist system in 1943, the National Diet gradually implemented a new lay judge system (裁判員, or "Saiban-in") from 2004 to 2009. This system, resembling more democratic systems in North American and European countries, calls upon six random common citizens to serve as inquisitorial judges alongside three professional judges. Together, they make up the judicial panel, who analyze and investigate evidence presented to them throughout the trial before ruling on guilt and sentencing. Reflecting this, Spoiler:the Jurist System seen at the end of Turnabout Succession is made up of six random jurors guided by Phoenix Wright, where the player from the sixth juror's perspective has to rule the defendant Guilty or Not Guilty.

Takumi revealed that as part of the game’s promotion, Capcom collaborated with the Japanese Ministry of Justice and gave a presentation about Apollo Justice: Ace Attorney at the ministry's head office, implying that the system's mandated inclusion in the game was political propaganda. Despite Capcom cooperating in the Japanese government's push for this new system and despite participation experiences being reported as positive and easy to understand, the reception to other aspects of the system were largely negative. Complaints included gradually more severe sentencing since its implementation, the risk of criminal penalties for lay judges publicly discussing confidential deliberation room details after trials come to an end, and most starkly, calling upon Japanese citizens to put aside time to participate in the system, who were more unwilling to do so. This decline in interest was attributed to the length of both lay judge trials and pre-trial proceedings increasing significantly over the next decade. Due to aging populations and people simply being unable to make these commitments, more citizens refused to serve or even show up to be vetted for serving, making it harder to fill out the jury. As a result of this reception, the Ace Attorney series has not used Spoiler:the MASON System and the Jurist System since, sticking with the series' traditional Initial Trial system in future games.

The button on Phoenix's hat is the same button worn by Ema Skye in the extra chapter added to the DS port of the first Ace Attorney game.

After Apollo catches Machi Tobaye lying, Lamiroir exclaims "What is wrong, Mr. Justice? Your eyes, they are quite fierce all of a sudden!" despite her being blind.

In the chapter "Turnabout Serenade", inside the Gavinners's dressing room are two references to the UK rock band "The Police". Examining the poster with the police officer on it will trigger a conversation about a band called The Police, and examining the red light on the ceiling will have Trucy talking about turning it on, with Apollo responding with "Don't turn on the red light", referencing the chorus to The Police's hit song, Roxanne.

In case three "Turnabout Serenade", on day 2 in the Wright Anything Agency if you examine the top hat, Apollo will say "That's one of those hats you pull things out of, right?". Trucy will then say "Of course! My hat's like a little universe! Bigger on the inside than on the outside!" which Apollo will reply saying "Hmm... That reminds me of a sci-fi show I used to watch."

This is a reference to the science fiction series Doctor Who and the spaceship the TARDIS which is bigger on the inside than on the outside.