Daisies of the Galaxy received a generally favorable response from critics.
Fred Kovey of PopMatters called it "a fine pop record in an era that seems uninterested in pop unless it’s marketed with dance steps and a quicky [sic] bio. Though not the equal of the best work of Stephen Merritt [sic] or Elliot Smith [sic], Daisies of the Galaxy is worthy of attention by alterna-pop fans and anyone else desperate for catchy music for grown-ups."Stephen Thomas Erlewine of AllMusic wrote: "Unlike its predecessor, the album doesn't play like [E's] private diary; instead, it feels as if one is rummaging through his sketchbook. And, like many sketchbooks, some moments have blossomed, and others remain just intriguing, unformed ideas. For the dedicated, it's worth sifting through the album to find the keepers, since there are enough moments of quirky genius. But not all longtime fans will find this rewarding, since [E] has spent more time in creating mood than crafting songs. There are very few melodies that resonate like his best work, and the stripped-down, yet eccentric production – sounding much like a cross between Jon Brion and Beck – never feels realized."
In a retrospective review for Stylus Magazine, Ben Woolhead described Daisies of the Galaxy as "a very special collection of songs indeed".