What was Caravaggio's dark-feathered deity of desire? The secrets that masterpiece uncovers about the rebellious artist

The youthful boy cries out as his head is forcefully held, a large digit pressing into his face as his father's powerful palm holds him by the throat. That scene from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking unease through the artist's harrowing portrayal of the tormented youth from the biblical narrative. It seems as if Abraham, commanded by God to kill his offspring, could break his spinal column with a solitary turn. Yet the father's chosen method involves the metallic steel knife he grips in his other hand, prepared to cut the boy's throat. A definite aspect remains – whoever modeled as the sacrifice for this astonishing piece displayed extraordinary acting ability. Within exists not just dread, surprise and begging in his shadowed gaze but also deep grief that a protector could abandon him so utterly.

He adopted a familiar biblical story and made it so fresh and visceral that its horrors seemed to happen directly in front of the viewer

Viewing before the painting, viewers recognize this as a real countenance, an accurate record of a young subject, because the same youth – identifiable by his disheveled hair and nearly dark eyes – appears in two additional paintings by Caravaggio. In each instance, that highly expressive visage dominates the composition. In John the Baptist, he peers playfully from the darkness while embracing a lamb. In Victorious Cupid, he smirks with a hardness acquired on Rome's alleys, his dark feathery wings sinister, a unclothed adolescent creating chaos in a affluent residence.

Amor Vincit Omnia, presently displayed at a British gallery, constitutes one of the most discomfiting masterpieces ever created. Viewers feel completely disoriented looking at it. The god of love, whose darts inspire people with often painful desire, is portrayed as a extremely tangible, brightly lit unclothed form, straddling toppled-over items that comprise musical instruments, a musical manuscript, plate armour and an architect's ruler. This pile of items resembles, deliberately, the geometric and construction gear scattered across the ground in the German master's engraving Melencolia I – save here, the melancholic mess is created by this smirking Cupid and the mayhem he can release.

"Love sees not with the vision, but with the mind, / And thus is winged Cupid painted sightless," wrote the Bard, just prior to this work was produced around the early 1600s. But the painter's Cupid is not blind. He stares straight at you. That face – ironic and ruddy-faced, staring with brazen assurance as he struts naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three images of the identical unusual-looking youth in Rome at the dawn of the 17th century, he was the highly acclaimed religious artist in a city ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been depicted numerous times before and make it so new, so raw and visceral that the terror appeared to be occurring directly in front of the spectator.

Yet there existed a different side to the artist, apparent as quickly as he arrived in the capital in the winter that ended 1592, as a artist in his early 20s with no mentor or patron in the urban center, only skill and audacity. Most of the paintings with which he caught the holy metropolis's eye were anything but devout. What may be the very earliest resides in the UK's art museum. A young man parts his red mouth in a yell of pain: while reaching out his filthy digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can discern the painter's gloomy chamber reflected in the cloudy liquid of the glass container.

The adolescent wears a rose-colored flower in his coiffure – a symbol of the sex trade in early modern painting. Venetian artists such as Tiziano and Palma Vecchio portrayed courtesans holding blooms and, in a work lost in the WWII but known through photographs, the master portrayed a famous woman prostitute, clutching a bouquet to her bosom. The meaning of all these botanical indicators is clear: intimacy for sale.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular boy in specific? It is a inquiry that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complex historical reality is that the artist was not the queer icon that, for instance, Derek Jarman put on film in his twentieth-century film Caravaggio, nor so entirely devout that, as some artistic scholars improbably assert, his Youth Holding Fruit is actually a likeness of Jesus.

His early works do make overt sexual suggestions, or including propositions. It's as if the painter, then a destitute youthful creator, identified with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in consideration, viewers might turn to an additional early work, the 1596 masterwork the god of wine, in which the god of wine stares coolly at you as he begins to untie the black sash of his garment.

A few years after Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was finally becoming nearly established with prestigious church projects? This profane non-Christian deity resurrects the sexual challenges of his initial paintings but in a increasingly powerful, unsettling manner. Half a century later, its hidden meaning seemed clear: it was a portrait of the painter's companion. A English traveller saw Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Cecco.

The artist had been deceased for about 40 years when this account was recorded.