The fresco can be seen as a portrayal of the Church Militant below, and the Church Triumphant above. A change in content between a study and the final fresco shows that the Disputa and The School of Athens can be seen as having a common theme: the revealed truth of the origin of all things, in other words the Trinity. This cannot be apprehended by intellect alone (philosophy), but is made manifest in the Eucharist.
The painting is built around the monstrance containing the consecrated Host, located on the altar. Figures representing the Triumphant Church and the Militant Church are arranged in two semicircles, one above the other, and venerate the Host. God the Father, bathed in celestial glory, blesses the crowd of biblical and ecclesiastical figures from the top of the composition. Immediately below, the resurrected Christ sits on a throne of clouds between the Virgin (bowed in adoration) and St John the Baptist (who, according to iconographic tradition, points to Christ). Prophets and saints of the Old and New Testament are seated around this central group on a semicircular bank of clouds similar to that which constitutes the throne of Christ. They form a composed and silent crowd and, although they are painted with large fields of colour, the figures are highly individuated.
At the bottom of the picture space, inserted in a vast landscape dominated by the altar and the eucharistic sacrifice, are saints, popes, bishops, priests and the mass of the faithful. They represent the Church which has acted, and which continues to act, in the world, and which contemplates the glory of the Trinity with the eyes of the mind. Following a fifteenth century tradition, Raphael has placed portraits of famous personalities, both living and dead, among the people in the crowd. Bramante leans on the balustrade at left; the young man standing near him has been identified as Francesco Maria Della Rovere; Pope Julius II, who personifies Gregory the Great, is seated near the altar Dante is visible on the right, distinguished by a crown of laurel. The presence of Savonarola seems strange, but may be explained by the fact that Julius II revoked Pope Alexander VI's condemnation of Savonarola (Julius was an adversary of Alexander, who was a Borgia).
The structure of the composition is characterized by extreme clarity and simplicity, which Raphael achieved through sketches, studies and drawings containing notable differences in pose. References to other artists are visible throughout the composition (the young Francesco Maria Della Rovere, for example, possesses a Leonardo-like physiognomy). But the layout, the gestures and the poses are original products of Raphael's research, which here reaches a degree of admirable balance and high expressive dignity.