What was Caravaggio's dark-feathered deity of love? The secrets this masterpiece uncovers about the rebellious genius

The youthful boy screams while his head is firmly held, a massive digit digging into his cheek as his parent's mighty hand holds him by the throat. This moment from Abraham's Sacrifice visits the Florentine museum, creating unease through Caravaggio's chilling portrayal of the tormented youth from the biblical narrative. It seems as if Abraham, commanded by God to kill his offspring, could snap his spinal column with a single turn. However Abraham's preferred approach involves the silvery grey knife he holds in his other palm, prepared to cut Isaac's throat. A certain aspect remains – whoever posed as Isaac for this astonishing piece demonstrated remarkable expressive skill. There exists not only dread, surprise and pleading in his darkened gaze but additionally profound grief that a protector could abandon him so completely.

He adopted a well-known scriptural story and transformed it so fresh and visceral that its terrors seemed to unfold right in view of you

Viewing before the painting, observers recognize this as a actual face, an accurate record of a young model, because the identical boy – identifiable by his tousled hair and almost dark pupils – appears in two other works by Caravaggio. In each case, that highly expressive visage dominates the scene. In John the Baptist, he peers mischievously from the darkness while embracing a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his dark plumed wings sinister, a unclothed child running chaos in a well-to-do dwelling.

Victorious Cupid, presently exhibited at a British museum, represents one of the most embarrassing artworks ever created. Observers feel completely unsettled looking at it. Cupid, whose darts inspire people with often painful longing, is shown as a very tangible, vividly illuminated unclothed form, straddling toppled-over items that include musical devices, a music manuscript, metal armor and an architect's ruler. This heap of possessions echoes, deliberately, the mathematical and architectural gear scattered across the floor in the German master's print Melancholy – save in this case, the gloomy mess is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the vision, but with the mind, / And thus is feathered Cupid painted sightless," penned Shakespeare, just before this painting was produced around 1601. But Caravaggio's god is not blind. He gazes straight at you. That face – ironic and ruddy-faced, staring with brazen confidence as he struts naked – is the same one that shrieks in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his three images of the same unusual-looking kid in the Eternal City at the start of the seventeenth century, he was the most acclaimed sacred artist in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was sought to adorn churches: he could take a biblical narrative that had been portrayed many times previously and render it so new, so unfiltered and physical that the terror appeared to be occurring directly before the spectator.

Yet there existed a different aspect to Caravaggio, apparent as quickly as he arrived in the capital in the cold season that ended the sixteenth century, as a artist in his early 20s with no teacher or supporter in the city, only talent and audacity. The majority of the works with which he caught the sacred metropolis's eye were everything but devout. What may be the absolute earliest resides in the UK's art museum. A youth parts his crimson mouth in a yell of agony: while reaching out his dirty fingers for a cherry, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see the painter's gloomy chamber mirrored in the murky liquid of the glass container.

The boy sports a pink flower in his hair – a symbol of the erotic commerce in early modern art. Venetian artists such as Tiziano and Palma Vecchio portrayed courtesans grasping blooms and, in a work lost in the second world war but known through photographs, the master represented a renowned woman prostitute, clutching a bouquet to her bosom. The meaning of all these floral signifiers is clear: intimacy for sale.

How are we to make of the artist's sensual portrayals of boys – and of a particular boy in specific? It is a question that has divided his interpreters since he achieved widespread recognition in the 1980s. The complex historical truth is that the artist was not the homosexual icon that, for instance, Derek Jarman put on screen in his 1986 film Caravaggio, nor so completely pious that, as some art scholars unbelievably assert, his Youth Holding Fruit is actually a portrait of Jesus.

His early works indeed offer overt erotic suggestions, or including offers. It's as if Caravaggio, then a destitute youthful artist, identified with Rome's sex workers, selling himself to live. In the Florentine gallery, with this thought in mind, observers might look to an additional initial creation, the 1596 masterpiece the god of wine, in which the god of alcohol gazes coolly at the spectator as he starts to undo the black sash of his garment.

A several years after the wine deity, what could have driven the artist to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last becoming nearly respectable with important church commissions? This profane non-Christian god revives the erotic challenges of his early works but in a more powerful, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of Caravaggio's companion. A English traveller saw the painting in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this adolescent was Cecco.

The artist had been dead for about 40 annums when this account was recorded.