For JoJo's Bizarre Adventure, Araki wanted to use a classical method as a base before introducing modern elements. As an example, he often draws in a realistic style but uses surreal colors. Araki has been aiming to draw real spirits in JoJo resulting in him going to the Kappa River in Tōno, Iwate, to get a better understanding of the concept. Araki claims to be inspired from the art of the 1980s, shading techniques in Western art, and classical paintings; the manga coloring is based on calculations rather than consistency, with Araki citing artists like Paul Gauguin as inspiration. He also claims mystery is the central theme of the manga, as he was fascinated by it as a child. Furthermore, Araki wanted to explore superpowers and energy in JoJo's Bizarre Adventure resulting in various concepts such as Hamon and Stands. He said that the supernatural basis of the fights in his series evened the battlefield for women and children to match up against strong men. For Stardust Crusaders in particular, Araki was influenced by role-playing games in designing the characters' skills. In creating the manga's generational story, Araki thought much about death and the legacy people leave behind in their lives for their descendants, after the death of his grandfather. He took inspiration from Roots: The Saga of an American Family and East of Eden. Araki focused on Roots for its family-centric story,[8] and he took the idea of intertwined destiny and rivalry between two families from East of Eden. He thought highly of stories that were well-received after changing protagonists, which influenced Araki's decision to kill Jonathan Joestar and write a generational story, passing on his "Spirit" to his own descendants.

 The characters had no models, except Jotaro Kujo, who was based on Clint Eastwood. Araki stated that he wanted to try a different type of main character for every part; for example, Part 1's Jonathan Joestar was a serious and honest person, whereas Part 2's Joseph Joestar was a trickster. Although their personalities are different, the two share a physical resemblance in order to have some continuity because it was unheard of in the 1980s for a main character to die in a Weekly Shōnen Jump series.] Araki's consistent focus on the Joestar family was intended to give a feeling of pride as well as the wonder and mystery surrounding the lineage.

Araki originally planned the series as a trilogy, with the final confrontation taking place in present-day Japan. However, Araki did not want Part 3 to be a tournament affair, which was popular in Weekly Shōnen Jump at the time, and therefore decided to make it a "road movie" inspired by Around the World in Eighty Days. With Part 4, Araki said that he moved away from "muscle men" as they fell out of popularity with readers and he wanted to focus more on fashion. When designing his characters' outfits, Araki considers both everyday fashion and "cartoonish, bizarre clothing that would be impractical in real life". For Part 6, Araki wrote a female protagonist for the first time which he found complicated, but also interesting due to the humanity she could possess. He later described Part 2's much earlier supporting character Lisa Lisa as fresh and "unheard of" in both manga and society in general for its time, and said it was exciting to challenge people's expectations with the female warrior-type. Having not specifically set out on creating a disabled character, Araki explained that Part 7's paraplegic Johnny Joestar was a natural result of wanting to show a character who could grow, both physically and mentally, during a race where "he would be forced not only to rely on other people, but horses as well."

 Araki uses unique onomatopoeia and poses in the series, which he attributes to his love for heavy metal and horror films. The poses, which are known in Japan as JoJo-dachi (ジョジョ立ち, lit. "JoJo standing"), are iconic on his book covers and panels, 

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