What exactly was Caravaggio's black-winged god of desire? The secrets this masterpiece uncovers about the rebellious artist

The youthful lad screams as his head is firmly held, a large thumb digging into his cheek as his parent's powerful hand holds him by the throat. That moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's harrowing portrayal of the suffering child from the scriptural account. The painting seems as if Abraham, instructed by God to kill his offspring, could break his spinal column with a single turn. However Abraham's preferred method involves the metallic grey knife he holds in his remaining palm, ready to slit the boy's neck. One certain element stands out – whomever modeled as the sacrifice for this astonishing piece displayed remarkable expressive skill. There exists not only dread, surprise and pleading in his shadowed gaze but additionally profound grief that a guardian could abandon him so completely.

The artist adopted a well-known scriptural tale and made it so vibrant and raw that its terrors seemed to unfold directly in view of you

Standing before the artwork, observers identify this as a actual face, an accurate record of a adolescent subject, because the same boy – recognizable by his tousled locks and almost black pupils – appears in several additional paintings by the master. In every instance, that richly emotional visage dominates the composition. In Youth With a Ram, he peers playfully from the darkness while holding a ram. In Victorious Cupid, he grins with a toughness acquired on the city's streets, his black feathery appendages sinister, a naked adolescent running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most embarrassing artworks ever created. Viewers feel totally unsettled looking at it. Cupid, whose darts fill people with often agonizing desire, is shown as a very tangible, vividly lit unclothed figure, standing over toppled-over items that include stringed devices, a music score, plate armor and an architect's T-square. This pile of items echoes, deliberately, the geometric and architectural equipment strewn across the ground in Albrecht Dürer's engraving Melancholy – except here, the melancholic disorder is created by this smirking deity and the turmoil he can unleash.

"Love sees not with the eyes, but with the mind, / And therefore is feathered Cupid painted sightless," penned the Bard, just before this work was produced around 1601. But the painter's Cupid is not unseeing. He stares directly at you. That face – ironic and rosy-cheeked, staring with brazen confidence as he poses unclothed – is the same one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his multiple images of the same distinctive-appearing youth in the Eternal City at the start of the 17th century, he was the highly celebrated sacred painter in a metropolis ignited by Catholic revival. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been portrayed many times before and make it so new, so unfiltered and physical that the horror seemed to be occurring directly in front of you.

However there was another aspect to Caravaggio, evident as quickly as he arrived in the capital in the winter that concluded 1592, as a artist in his early 20s with no mentor or patron in the urban center, only talent and boldness. Most of the works with which he captured the holy city's eye were anything but devout. That could be the absolute earliest resides in London's National Gallery. A young man opens his red mouth in a scream of agony: while reaching out his dirty fingers for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: viewers can discern the painter's gloomy room mirrored in the cloudy waters of the transparent container.

The adolescent sports a pink flower in his hair – a symbol of the sex trade in early modern painting. Northern Italian artists such as Titian and Palma Vecchio depicted courtesans grasping blooms and, in a work destroyed in the second world war but known through images, the master portrayed a renowned female courtesan, clutching a posy to her chest. The message of all these botanical signifiers is obvious: sex for purchase.

What are we to make of Caravaggio's erotic depictions of youths – and of a particular boy in specific? It is a question that has split his commentators since he achieved mega-fame in the 1980s. The complicated historical truth is that the painter was neither the queer hero that, for example, the filmmaker put on screen in his twentieth-century film Caravaggio, nor so entirely devout that, as some artistic scholars improbably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His initial works indeed offer overt sexual implications, or including offers. It's as if Caravaggio, then a penniless young artist, identified with the city's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, observers might look to an additional initial work, the 1596 masterwork the god of wine, in which the deity of alcohol gazes calmly at the spectator as he starts to untie the black sash of his garment.

A several annums following the wine deity, what could have driven Caravaggio to paint Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was at last becoming almost established with prestigious church commissions? This unholy non-Christian deity revives the erotic provocations of his early paintings but in a increasingly intense, unsettling manner. Fifty years later, its hidden meaning seemed obvious: it was a representation of the painter's companion. A English traveller viewed Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this adolescent was Cecco.

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