According to producer Kenichi Hashimoto, Apollo Justice: Ace Attorney Trilogy was Capcom's first text adventure game to run on their RE Engine, which proved to be a hurdle in their attempts to port and configure the original games into the engine.

While the first three games in the series originated on the single-screen Game Boy Advance and were later ported to the dual screen Nintendo DS, the next three games in this collection needed to be ported from a dual screen handheld to modern platforms with a single screen. Producer Kenichi Hashimoto noted that this conversion process had its challenges, as the team needed to completely redesign the user interface and tweak each game's programming to make sure it was functional for controller users, PC players using a mouse and keyboard, and those using a touch screen format via the Nintendo Switch.

According to series translator Janet Hsu, the games that make up the "Apollo Justice Trilogy" were grouped together as such because Apollo Justice had a more prominent ongoing character arc compared to Phoenix Wright, despite Apollo Justice's name being in the title of only one game outside of Japan. Hsu felt that this would have been less confusing to some if the games were instead released internationally with sequential numbers like the game's Japanese title, Gyakuten Saiban. Apollo Justice Ace Attorney Trilogy producer Kenichi Hashimoto believed that Apollo could still be the focus of future games, but acknowledged this was yet to be determined.

None of the original sound data was reused from Apollo Justice: Ace Attorney for this re-release. Every sound effect in the game was remade from scratch using the original game's sound data as reference material, and previously unreleased sound data was used for the background music.

According to localizer Benjamin Ruppin, who worked on the French localization of Phoenix Wright: Ace Attorney - Spirit of Justice for this collection, the Khura'inese character names were the most challenging to translate to French due to their exotic sound masking otherwise easy-to-understand puns. In particular, Ruppin revealed his least favorite name to translate was Pees'lubn Andistan'dhin (A.K.A. peace, love and understanding).

A running gag throughout the Ace Attorney series involves the protagonist and his assistant having a conversation about the difference between a ladder and a stepladder. First occurring in "Turnabout Samurai", the third case of Phoenix Wright: Ace Attorney, a stepladder has appeared in at least one location in each game to date (with the exception of The Great Ace Attorney: Adventures) for the sole purpose of continuing the tradition. The conversation generally goes as follows: after examination, the protagonist and one of their partner characters engage in a debate about the usage of the words "ladder" and "stepladder", and the difference between the two. Usually, one will accuse the other of being too absorbed in the details instead of looking at the big picture to realize that they both serve roughly the same function, to which the latter's response will often vary. Additionally, similar gags in regards to other items in the series have also been used, particularly in The Great Ace Attorney games, which primarily use a variant of the debate involving the difference between a shovel and a spade instead.

Within the various re-releases of the Ace Attorney games, an achievement is added that can be unlocked for engaging in every "ladder vs. stepladder" debate within the games featured in that collection. In the case of The Great Ace Attorney Chronicles, a second achievement for engaging in every "shovel vs. spade" debate within the two games is also included.