Akira Yasui, the game's director, and Taro Yoko, who had directed the original game, suffered from creative differences, with the result that Yoko termed their relationship on the project as a "love-hate" story in a 2013 interview concerning the series. Their relationship inspired one of the stories created for an in-game weapon. Yoko was also not as involved in creating the narrative as he had been in Drakengard, being mostly tied up with another project. One of the decisions Yasui made was to make Drakengard 2 far more colorful than the previous game, wanting to do something that was the "opposite" of Drakengard. The initial concept Yoko created for the game was a space adventure involving dragons, but this was vetoed at an early stage. Yoko's job was as the game's video editor.
In contrast to the previous game, the game contained far less of the mature themes found in the original. Shiba, speaking in a 2013 interview, said that the reason for this was that Square Enix, the company's Japanese publisher, wanted that aspect toned down to make a more mainstream game.