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A youthful lad cries out as his skull is forcefully held, a massive thumb pressing into his face as his parent's powerful palm holds him by the throat. This scene from The Sacrifice of Isaac visits the Florentine museum, creating unease through the artist's harrowing rendition of the suffering child from the biblical account. The painting appears as if the patriarch, commanded by God to sacrifice his son, could break his spinal column with a single twist. Yet Abraham's preferred method involves the metallic steel blade he grips in his other hand, ready to slit Isaac's throat. One certain element remains – whomever modeled as the sacrifice for this astonishing work demonstrated extraordinary expressive ability. Within exists not just fear, shock and begging in his darkened eyes but also profound grief that a guardian could abandon him so completely.

He took a well-known biblical tale and made it so vibrant and raw that its terrors seemed to happen directly in front of you

Viewing in front of the painting, observers identify this as a real countenance, an accurate record of a young subject, because the identical boy – recognizable by his disheveled locks and nearly dark pupils – features in several other paintings by Caravaggio. In every instance, that richly emotional face commands the composition. In John the Baptist, he peers mischievously from the darkness while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his dark feathery wings sinister, a unclothed adolescent creating riot in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most discomfiting masterpieces ever created. Observers feel totally disoriented looking at it. The god of love, whose darts fill people with often painful longing, is shown as a extremely tangible, brightly lit unclothed form, straddling toppled-over items that comprise stringed instruments, a music manuscript, plate armour and an builder's T-square. This heap of items resembles, intentionally, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's print Melancholy – except in this case, the gloomy mess is caused by this smirking deity and the turmoil he can release.

"Affection sees not with the vision, but with the soul, / And therefore is winged Cupid depicted sightless," wrote Shakespeare, shortly before this work was produced around the early 1600s. But Caravaggio's god is not unseeing. He gazes straight at the observer. That countenance – sardonic and ruddy-faced, looking with bold confidence as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As the Italian master created his three images of the identical distinctive-looking kid in the Eternal City at the start of the 17th century, he was the highly acclaimed religious artist in a city ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could take a biblical narrative that had been portrayed many times previously and make it so new, so raw and visceral that the horror seemed to be occurring directly in front of the spectator.

Yet there was a different side to the artist, evident as quickly as he came in the capital in the cold season that concluded 1592, as a painter in his early 20s with no teacher or patron in the urban center, just talent and boldness. Most of the works with which he captured the sacred city's eye were everything but holy. What may be the very first hangs in the UK's National Gallery. A youth parts his red lips in a scream of pain: while stretching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: observers can see Caravaggio's dismal room mirrored in the murky liquid of the glass container.

The adolescent wears a pink flower in his coiffure – a symbol of the sex trade in early modern art. Northern Italian painters such as Titian and Palma Vecchio portrayed courtesans grasping blooms and, in a painting destroyed in the WWII but known through photographs, the master portrayed a renowned woman courtesan, holding a posy to her chest. The meaning of all these floral signifiers is clear: intimacy for sale.

How are we to interpret of Caravaggio's erotic depictions of youths – and of a particular adolescent in particular? It is a question that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complex past reality is that the painter was not the queer hero that, for instance, the filmmaker put on film in his 1986 movie about the artist, nor so completely devout that, as certain art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His initial paintings indeed make overt sexual suggestions, or even offers. It's as if the painter, then a penniless young creator, aligned with the city's sex workers, offering himself to live. In the Uffizi, with this idea in consideration, observers might turn to an additional early work, the sixteenth-century masterpiece the god of wine, in which the deity of wine gazes coolly at you as he starts to undo the black sash of his garment.

A few years following Bacchus, what could have driven the artist to paint Victorious Cupid for the art collector the nobleman, when he was finally growing nearly established with prestigious church projects? This unholy non-Christian god resurrects the sexual provocations of his initial works but in a more powerful, unsettling way. Fifty years later, its hidden meaning seemed clear: it was a representation of Caravaggio's companion. A British traveller saw the painting in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this boy was Francesco.

The painter had been dead for about 40 annums when this story was documented.