Since 2004, the studio's productions and staff have been broadly influenced by director Akiyuki Shinbo, whose visual style and avant-garde cinematography are featured in works including Hidamari Sketch (2007), Sayonara, Zetsubou-Sensei (2007), the Monogatari series (2009–present), Puella Magi Madoka Magica (2011), Nisekoi (2014), and March Comes In Like a Lion (2016).

[11] In 1995, the studio moved to producing full-length series, starting with Juuni Senshi Bakuretsu Eto Ranger.

[13] Mitsutoshi Kubota, a studio color designer turned production manager at the time, met with the two,[13] and from then they would collaborate on several more projects together, such as Shaft producing an episode of Nakamura and Triangle Staff's Kino's Journey television series,[13] and Nakamura later directing a television series and Kino's Journey film at the studio.

[16] In 2003 and 2004, the studio produced an adaptation of the visual novel Popotan,[17] and later This Ugly yet Beautiful World, an original series co-produced with Gainax and director Shouji Saeki.

During the mid-to-late 2000s, the studio brought on a number of new directors and creators, including Ryouki Kamitsubo, Naoyuki Tatsuwa, Kenichi Ishikura, Yukihiro Miyamoto, Shinichi Omata, Tomoyuki Itamura, and Gekidan Inu Curry.

Kamitsubo and Oonuma, however, left by the end of the decade, with the latter joining Silver Link where he established himself in a similar role to Shinbo's.

It gained a cult-like following among fans in both Japan and the West for its narrative and "visually striking" animation and artistic qualities.

[31] Following Bakemonogatari, the studio produced yet another critical and financial hit two years later with Puella Magi Madoka Magica.

[35] In 2012, the studio returned to animating the Monogatari series with Nisemonogatari, albeit with director Tomoyuki Itamura in place of Oishi.

Tatsuya Oishi disappeared from the public spotlight in the early 2010s after he began production on the Kizumonogatari film trilogy, which was released in 2016 and 2017.

[38] Shaft's animation work on the trilogy has been praised as being uniquely experimental with 2D and CG effects, which some reviewers described as not always mixing well, but has nonetheless been called "gorgeous.

Yuki Yase left after directing The Beheading Cycle: The Blue Savant and the Nonsense Bearer (2016–17),[41] taking animation producer Kousuke Matsunaga with him to work on Fire Force at David Production (as well as CG director Shinya Takano and at-the-time production assistants Reo Honjouya and Hisashi Sugawara); Tomoyuki Itamura, who had directed the rest of the Monogatari series after Oishi's commitment to Kizumonogatari, left after the production of Owarimonogatari II (2017);[42] Izumi Takizawa, a color designer with the studio since the late 90s, followed Itamura.

[49] Shinbo returned to the director's chair in 2021 with his adaptation of Pretty Boy Detective Club, which he co-directed alongside Ootani.

Whereas he had previously been involved in every major production since 2004 (with the exception of their co-productions with Gainax and the two works directed by Ryūtarō Nakamura), various other affiliated directors began to take up the mantle—most notably Miyamoto and Saeki.

Pre-production of the series started in fall of 2022 following the end of Luminous Witches and RWBY: Ice Queendom when Aniplex producer Tatsuya Ishikawa approached the studio about continuing the adaptation.

[64] Agreeing, studio president Kubota selected Midori Yoshizawa, who had been directing at Shaft for nearly a decade by that point, as the new series director under Shinbo.

[64] The same year, Shaft was announced to be producing an adaptation of HundredBurger's Ninja to Koroshiya no Futarigurashi manga series.

[5] They each brought separate stylistic strengths that contributed to the eventual "Shaft style" the studio embraced, despite the fact that neither Oonuma nor Oishi had much prior experience as directors.

[5] Oonuma and Oishi's success with the studio is in part due to the "mentorship" system created at Shaft, which was centered around Shinbo.

[5][70] Tatsuwa, in contrast to the others, maintained series with less visual surrealism, albeit he continued to use several of the stylistic elements from the other directors.

[75] Shinichirou Etou, who had been working at the company for three years as a production assistant, was asked to set up the department due to his experience in CG from when he attended Japan Electronics College [ja].

[75] Pretty Boy Detective Club also used the name Shaft Umegumi for its opening animation production credit, a humorous title given to director Yasuomi Umetsu and part of his team at the studio who produced the opeing while working on their own project, the then-unannounced Virgin Punk.

[80] Madoka Magica screenwriter Gen Urobuchi described the work environment as giving him a level of freedom he'd never had before, and that "I did not think I could have written this screenplay in any other place", and both original character designer Ume Aoki and alternate space designers Gekidan Inu Curry have expressed similar perspectives.

[87] For this reason, Okada set up the schedule so that the film was split into five units (A through E), and each one would be worked on in order rather than different parts moving forward at different times.

According to Shinbo, the first storyboard drawn for the studio and his newfound collaboration, Tsukuyomi: Moon Phase episode 1, was 308 cuts.

[88] Considering the time and budget series like Hidamari Sketch had, Shinbo mentioned that he doesn't think any other studio would allow as many cuts and as many corrections to the home video release versions as Shaft.

[90] Kubota has also emphasized a particular focus on putting full studio effort into each of their works, and not increasing the number of productions purely to satiate demand.

[82] The uniqueness of Shaft's production system compared to other anime studios, with several directors and specialized roles per most series, has also introduced certain problems.