Writing for AllMusic, Scott Yanow gave the album 4.5 out of 5 stars, stating that "During the two lengthy pieces, [Jimmy] Lyons' passionate solos contrast with [Bill] Dixon's quieter ruminations while the music in general is unremittingly intense."[3]
The authors of The Penguin Guide to Jazz awarded the album 4 stars, calling it "an all but flawless record," and commenting: "Dark, difficult, unique, yet operating at an artful tangent to some of the other 'difficult' Blue Note music of the period, this is Taylor at his most devious."[5]
Writing for Vinyl Me Please, Brian Josephs stated: "Conquistador!... swerves away from Unit Structures' fire and evokes the coolness of its cover, which features a turtlenecked Taylor slightly out of focus, hiding behind shades as he mysteriously stares into the distance. The musical elements don’t combust as much as they melt into each other: Horns swell shrilly at the borders to add haunted textures, while Andrew Cyrille's amorphous rhythms tie the masterwork together. Even without Unit Structures as its contrast, Conquistador! still stands as a great testament to this sui generis collective."[7]
In 2008, The New Yorker placed it at number 87 on the "100 Essential Jazz Albums" list.[8]