The Desert Transcendentalistexhibition itself was supported in part by an award from the National Endowment for the Arts, signaling significant federal recognition of her cultural importance. The Phoenix Art Museum organized the exhibition, which was supported other partners, including The Andy Warhol Foundation for the Visual Arts.

Agnes’s work is now featured in major collections and ongoing displays, such as the Museum of Modern Art (MoMA) in New York and the Hilbert Museum of California Art.

In January 2025, the Daughters of the American Revolution (DAR) celebrated Pelton’s 144th birthday by placing a commemorative plaque at her former home in Cathedral City, which is also a designated historic site.

In recognition of Agnes’s legacy, the city of Cathedral City designated the nearby alleyway and street as Agnes Pelton Way. Local artists have been commissioned to paint murals in her former neighborhood, Cathedral City Cove, to commemorate her history and the artist colony she helped lead.

The Agnes Pelton Society hosts annual events, such as the inaugural Pelton House Museum Day (first held in 2019), which includes docent-led tours of her historic home and meditation gardens.

Pelton is recognized as a "Luminary" by the National Association of Women Artists (NAWA), an honor given to pioneering women in the arts.

Her work has been the focus of recent major scholarly studies, most notably in Erika Doss’s Spiritual Moderns: Twentieth Century Artists and Religion(2022), which positions her alongside figures like Wassily Kandinsky and Hilma af Klint.

While she was famously denied a Guggenheim fellowship in 1932, recent scholarly work and major museum retrospectives (like the Whitney's) are frequently cited as the ultimate "critical vindication" of her rejected application.

Since December 2023, MoMA has featured Pelton in its Nature Symbolized gallery, cementing her place in the permanent narrative of modern art.