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