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A young boy cries out while his skull is forcefully gripped, a massive digit pressing into his face as his parent's mighty palm holds him by the throat. That moment from Abraham's Sacrifice visits the Florentine museum, evoking unease through Caravaggio's harrowing rendition of the suffering youth from the biblical account. It seems as if the patriarch, commanded by the Divine to kill his son, could snap his spinal column with a single turn. However the father's preferred approach involves the silvery grey blade he grips in his other hand, ready to slit the boy's throat. A definite aspect remains – whomever modeled as the sacrifice for this breathtaking piece demonstrated remarkable acting ability. Within exists not just dread, shock and pleading in his darkened gaze but also profound sorrow that a guardian could betray him so completely.

The artist adopted a familiar scriptural tale and transformed it so fresh and visceral that its horrors appeared to happen right in view of you

Standing before the painting, viewers recognize this as a actual countenance, an accurate depiction of a young model, because the identical boy – recognizable by his disheveled locks and nearly black eyes – appears in several other works by Caravaggio. In every instance, that richly expressive face dominates the scene. In Youth With a Ram, he peers playfully from the shadows while embracing a lamb. In Victorious Cupid, he grins with a hardness acquired on Rome's alleys, his black plumed wings demonic, a unclothed adolescent running riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a British museum, represents one of the most discomfiting masterpieces ever painted. Viewers feel completely disoriented gazing at it. The god of love, whose darts inspire people with often agonizing longing, is portrayed as a very tangible, vividly illuminated unclothed figure, straddling toppled-over objects that include stringed devices, a musical score, metal armour and an builder's T-square. This pile of possessions resembles, intentionally, the geometric and architectural gear strewn across the floor in the German master's print Melencolia I – except here, the melancholic disorder is caused by this grinning deity and the mayhem he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted blind," wrote the Bard, just before this work was produced around 1601. But Caravaggio's god is not unseeing. He stares directly at the observer. That face – ironic and ruddy-faced, staring with brazen confidence as he struts naked – is the same one that screams in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his multiple portrayals of the identical distinctive-looking youth in Rome at the dawn of the 17th century, he was the highly celebrated religious painter in a metropolis ignited by religious revival. The Sacrifice of Isaac demonstrates why he was sought to decorate sanctuaries: he could adopt a scriptural narrative that had been depicted numerous times before and make it so new, so raw and visceral that the terror appeared to be happening immediately in front of you.

Yet there was another aspect to Caravaggio, evident as quickly as he arrived in Rome in the cold season that concluded 1592, as a painter in his early 20s with no mentor or supporter in the urban center, only skill and boldness. Most of the works with which he caught the sacred metropolis's eye were anything but holy. That may be the absolute first resides in the UK's National Gallery. A youth opens his red mouth in a scream of pain: while reaching out his dirty fingers for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's dismal room reflected in the cloudy liquid of the transparent vase.

The adolescent sports a rose-colored blossom in his hair – a symbol of the erotic commerce in early modern art. Northern Italian artists such as Titian and Palma Vecchio depicted prostitutes grasping blooms and, in a painting destroyed in the WWII but known through photographs, Caravaggio represented a famous woman prostitute, holding a bouquet to her chest. The meaning of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of the artist's sensual portrayals of boys – and of one adolescent in specific? It is a inquiry that has split his commentators since he achieved mega-fame in the twentieth century. The complicated historical truth is that the painter was not the queer hero that, for example, the filmmaker presented on film in his twentieth-century movie about the artist, nor so completely pious that, as certain artistic scholars improbably assert, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial works indeed offer explicit erotic implications, or including propositions. It's as if Caravaggio, then a penniless youthful creator, identified with Rome's sex workers, selling himself to live. In the Uffizi, with this idea in mind, observers might look to another early work, the 1596 masterwork Bacchus, in which the deity of alcohol gazes coolly at you as he begins to untie the dark sash of his garment.

A several years after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was at last growing nearly established with prestigious ecclesiastical projects? This profane non-Christian god resurrects the erotic provocations of his early works but in a increasingly powerful, unsettling way. Fifty years afterwards, its secret seemed obvious: it was a representation of the painter's companion. A English visitor saw Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] own boy or servant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty annums when this story was recorded.