Devotional images of the Madonna and Child were a mainstay of Neroccio's workshop. Working from a standard half-length format, the artist altered the composition by adding different saints according to the wishes of his clients. Here, he has inserted John the Baptist, who carries a scroll that proclaims the coming of Christ, and Mary Magdalene, who holds the jar of oil with which she anointed the feet of Jesus.

The infant Christ's nudity expresses his humanity, and therefore, the possibility of his suffering and death.

Amid the ferment of ideas and styles circulating in central and northern Italian art in the late 15th century, certain painters perpetuated a more old-fashioned aesthetic. The Sienese artist Neroccio was one of these. Not surprisingly, the 16th-century biographer Giorgio Vasari does not mention him in his lives of Renaissance artists. Nevertheless, the Clowes Madonna marks a sharp departure from the lyrical and provincial style of Neroccio's early career. While retaining the half-length format of devotional paintings of the Virgin with saints, Neroccio also borrows stylistic elements from the better-known Tuscan artists Sandro Botticelli and Luca Signorelli. The graceful modeling, inspired by Botticelli, and the rigid shading and coloristic treatment taken from Signorelli suggest a late 1490s date for the Clowes Madonna. In addition, the pronounced monumentality of the figures owes something to Florentine sculpture. Neroccio, himself a sculptor, kept a gesso copy of a Donatello Madonna in his workshop.

The presence of John the Baptist and Mary Magdalene, certainly dictated by the patron, acquires a complex theological resonance alongside the lively Christ child. Both saints attested to the divinity of Jesus, whose humanity is represented by his exposed genitalia. These seemingly contradictory elements underscore the mystery and dogma of the Incarnation.

The nudity of Christ is, as it were, the mark of his humanity; he now resembles the children of humankind.
-Medievalist Emile Mâle, 1908