Director Takeshi Yamazaki knew from the start that he wanted all three player characters to have their own motivations and purposes that would play out throughout the game. At one point, he even considered having five lawyers in the game, on account of Dual Destinies being the fifth game in the series. He later stated that the idea was "crazy and overly ambitious", and that they had dodged a bullet by not doing it.

Edgeworth's design for the game went through many iterations. In the first design, he had large frills that went down to his thighs. In other designs, he had grown facial hair. In the end, Edgeworth retained an "elegant" look, with rolled back sleeves and vest, and sporting a longer coat and a pair of glasses, appearing more like his father.

Juniper Woods' stage outfit for when she was going to sing the Guitar's Serenade during the Gavinner's return concert is almost exactly the same as Lamiroir's, who originally sang the same song in Ace Attoreny: Apollo Justice. Weirdly enough, neither Apollo, Trucy nor Klavier make any mentions of the fact despite having met Lamiroir.

The artbook "The Art of Phoenix Wright: Ace Attorney - Dual Destinies" by Udon Entertainment expands upon this. In-universe, the similarities are purely coincidental, as Juniper just so happened to design the exact same costume that Lamiroir wore during the previous game. Out-of-universe, however, it was done to tie into the sub-plot about Juniper's crush on Apollo Justice, as it allowed for a cutscene where she gains "brownie points" with Justice, who is a fan of Lamiroir's music.

The TV guide mentioning a wrestling match found during the second case is a possible reference to the Twilight book/movie series. It's about a match between Howlin' Wolf and Pretty Boy Vampire, hosted by Timothy Twilight.

Apollo's ringtone is a remix of "The Guitar's Serenade" from Ace Attorney: Apollo Justice. The performance of this song, by The Gavinners featuring Lamiroir, was central to the "Turnabout Serenade" case in that game.

During Case 4, A Cosmic Turnabout, during Yuri Cosmos' breakdown (while his segway is malfunctioning), several of the stars that appear on screen resemble the Starman power-up item from the Mario series.

In the DLC Case "Turnabout Reclaimed", when Phoenix and Athena investigate Shipshape Aquarium's shark cannon near Orla's tank, Phoenix remarks about the cannon balls looking like fish eggs. This gets Athena to suggest they should be baby sharks and says, "I can see it now! The drama! The mayhem! The whirlwind of teeth!" Phoenix then thinks, "A tornado of sharks? Not even Hollywood could conjure up something that insane."

This is a reference to the 2013 made-for-TV film Sharknado, which features a tornado of sharks.

Game designer Yuki Nakamura, who was in charge of writing the DLC episode "Turnabout Reclaimed", used the concept of "lighthearted fun" to set it apart from the episodes in the base game. The episode featuring an orca and taking place in an aquarium was the first thing she decided on, but she struggled to come up with the rest of the story. One scrapped idea had the orca stealing treasure from the aquarium and attacking people by the shore as it escaped to sea, with the mystery involving the reason for the orca's behavior. The draft for this version of the episode opened with Bobby Fulbright and some guards vaguely referring to somebody escaping. This was intended to mislead players into thinking that they were referring to Simon Blackquill, before it was ultimately revealed to be the orca.

Phoenix Wright: Ace Attorney - Dual Destinies’ English release is known for having many more typos and grammatical errors than previous entries with as much as 30 instances being catalogued throughout the whole game.