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A youthful boy screams while his skull is forcefully gripped, a large digit digging into his face as his parent's powerful palm grasps him by the neck. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through Caravaggio's chilling rendition of the tormented child from the biblical account. It appears as if Abraham, commanded by God to sacrifice his offspring, could break his neck with a solitary turn. However the father's chosen approach involves the silvery grey blade he holds in his other hand, prepared to slit the boy's neck. A definite element stands out – whoever modeled as the sacrifice for this breathtaking work demonstrated extraordinary acting ability. Within exists not only fear, surprise and pleading in his shadowed eyes but also deep sorrow that a guardian could abandon him so completely.

He took a well-known scriptural tale and made it so vibrant and visceral that its horrors seemed to unfold directly in front of you

Viewing before the painting, observers recognize this as a real face, an accurate depiction of a adolescent subject, because the identical youth – identifiable by his disheveled locks and almost black eyes – features in several other works by the master. In each instance, that highly emotional face commands the scene. In John the Baptist, he peers mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on the city's streets, his black plumed appendages demonic, a naked child running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, represents one of the most discomfiting masterpieces ever created. Viewers feel totally unsettled looking at it. The god of love, whose arrows fill people with often painful desire, is portrayed as a extremely real, vividly lit unclothed figure, straddling toppled-over objects that comprise stringed instruments, a music manuscript, metal armor and an architect's T-square. This pile of possessions echoes, intentionally, the geometric and architectural equipment scattered across the floor in the German master's print Melencolia I – except here, the gloomy disorder is caused by this grinning Cupid and the mayhem he can release.

"Affection sees not with the eyes, but with the mind, / And thus is feathered Love painted blind," wrote the Bard, just prior to this painting was produced around the early 1600s. But Caravaggio's god is not blind. He gazes directly at the observer. That countenance – ironic and rosy-faced, looking with brazen assurance as he struts unclothed – is the same one that shrieks in fear in Abraham's Test.

As the Italian master created his multiple portrayals of the same unusual-appearing youth in Rome at the dawn of the 17th century, he was the highly acclaimed religious artist in a metropolis ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate sanctuaries: he could take a biblical narrative that had been depicted numerous occasions before and render it so new, so unfiltered and visceral that the horror seemed to be occurring immediately in front of the spectator.

Yet there existed another side to Caravaggio, apparent as soon as he came in the capital in the winter that ended the sixteenth century, as a painter in his initial 20s with no mentor or supporter in the urban center, only talent and audacity. Most of the paintings with which he captured the holy city's attention were anything but devout. What could be the absolute earliest hangs in the UK's art museum. A youth opens his red mouth in a scream of agony: while reaching out his filthy digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can see the painter's dismal chamber mirrored in the murky liquid of the transparent vase.

The adolescent sports a pink flower in his hair – a emblem of the erotic trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping flowers and, in a painting destroyed in the second world war but known through images, Caravaggio represented a renowned female courtesan, holding a bouquet to her chest. The meaning of all these floral signifiers is clear: sex for purchase.

How are we to interpret of the artist's sensual depictions of youths – and of a particular boy in particular? It is a question that has divided his commentators since he gained mega-fame in the 1980s. The complicated past reality is that the painter was not the queer hero that, for instance, Derek Jarman put on screen in his 1986 movie Caravaggio, nor so entirely pious that, as some art scholars improbably claim, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His initial works do offer explicit sexual suggestions, or even offers. It's as if the painter, then a destitute young artist, identified with the city's prostitutes, selling himself to live. In the Florentine gallery, with this thought in consideration, viewers might look to another initial work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares coolly at you as he starts to undo the black ribbon of his garment.

A several years following Bacchus, what could have motivated Caravaggio to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was at last becoming nearly established with prestigious church projects? This profane pagan god resurrects the sexual provocations of his initial works but in a more intense, unsettling way. Half a century later, its secret seemed obvious: it was a representation of the painter's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] own youth or servant that laid with him". The identity of this boy was Cecco.

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