What exactly was the black-winged deity of love? The insights that masterwork reveals about the rebellious artist

The youthful boy screams as his head is forcefully gripped, a massive thumb pressing into his face as his father's powerful hand grasps him by the neck. This moment from Abraham's Sacrifice visits the Florentine museum, creating distress through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. It appears as if the patriarch, instructed by the Divine to kill his son, could snap his spinal column with a solitary turn. Yet the father's preferred approach involves the silvery grey knife he holds in his remaining palm, ready to cut Isaac's neck. One certain element remains – whoever modeled as Isaac for this breathtaking piece demonstrated remarkable expressive skill. Within exists not just fear, surprise and begging in his shadowed eyes but additionally deep grief that a protector could betray him so utterly.

The artist adopted a well-known scriptural tale and transformed it so fresh and raw that its horrors seemed to happen directly in view of you

Standing before the painting, observers identify this as a real countenance, an precise record of a young subject, because the identical youth – identifiable by his tousled hair and almost dark eyes – features in several other paintings by the master. In every case, that richly emotional face dominates the scene. In Youth With a Ram, he gazes playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on the city's alleys, his black feathery appendages sinister, a naked child creating riot in a well-to-do residence.

Victorious Cupid, currently exhibited at a London gallery, represents one of the most discomfiting artworks ever painted. Viewers feel completely unsettled gazing at it. The god of love, whose arrows inspire people with often painful longing, is shown as a extremely real, brightly illuminated unclothed form, standing over toppled-over items that include musical instruments, a musical score, plate armour and an architect's T-square. This pile of possessions resembles, deliberately, the mathematical and architectural equipment strewn across the floor in Albrecht Dürer's print Melancholy – except here, the melancholic mess is caused by this grinning Cupid and the mayhem he can release.

"Affection sees not with the eyes, but with the soul, / And therefore is winged Cupid painted blind," wrote Shakespeare, shortly before this work was created around the early 1600s. But the painter's Cupid is not unseeing. He stares straight at the observer. That face – sardonic and ruddy-cheeked, looking with bold confidence as he struts unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

As the Italian master painted his three images of the same unusual-looking youth in Rome at the dawn of the seventeenth century, he was the most celebrated religious artist in a city ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to adorn sanctuaries: he could take a scriptural story that had been portrayed numerous occasions previously and render it so fresh, so unfiltered and visceral that the terror seemed to be happening immediately before the spectator.

Yet there was another side to Caravaggio, apparent as soon as he arrived in Rome in the cold season that ended the sixteenth century, as a artist in his initial twenties with no teacher or supporter in the city, only talent and audacity. Most of the works with which he caught the sacred metropolis's eye were anything but devout. What could be the very earliest resides in the UK's art museum. A young man opens his red lips in a yell of agony: while reaching out his filthy fingers for a fruit, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can discern Caravaggio's gloomy chamber mirrored in the cloudy liquid of the transparent container.

The boy wears a pink blossom in his coiffure – a symbol of the erotic trade in early modern art. Northern Italian artists such as Titian and Palma Vecchio depicted prostitutes holding flowers and, in a work destroyed in the second world war but known through images, Caravaggio portrayed a renowned woman prostitute, clutching a posy to her chest. The message of all these botanical signifiers is clear: intimacy for sale.

What are we to make of the artist's erotic portrayals of boys – and of a particular adolescent in particular? It is a question that has divided his commentators since he achieved widespread recognition in the twentieth century. The complex past truth is that the painter was not the homosexual icon that, for example, Derek Jarman presented on film in his twentieth-century movie Caravaggio, nor so completely devout that, as some artistic scholars unbelievably assert, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early paintings do offer explicit sexual implications, or even offers. It's as if Caravaggio, then a penniless young artist, aligned with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in consideration, viewers might look to an additional early work, the 1596 masterpiece Bacchus, in which the deity of alcohol gazes calmly at the spectator as he starts to untie the dark ribbon of his robe.

A several years following Bacchus, what could have motivated Caravaggio to paint Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with important church projects? This profane pagan god revives the sexual challenges of his initial works but in a more powerful, uneasy way. Fifty years later, its secret seemed obvious: it was a representation of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] own boy or servant that slept with him". The name of this boy was Francesco.

The artist had been deceased for about forty annums when this story was documented.