What was Caravaggio's dark-feathered god of love? The secrets that masterpiece uncovers about the rogue genius

A youthful boy screams as his head is firmly gripped, a massive digit pressing into his face as his parent's mighty palm holds him by the throat. This scene from The Sacrifice of Isaac visits the Florentine museum, creating unease through Caravaggio's harrowing portrayal of the suffering youth from the biblical account. The painting appears as if the patriarch, instructed by God to kill his son, could snap his neck with a single twist. Yet the father's preferred approach involves the silvery grey knife he grips in his other hand, prepared to slit the boy's neck. One definite aspect remains – whomever posed as Isaac for this astonishing work displayed extraordinary acting ability. There exists not just dread, shock and begging in his darkened eyes but additionally deep sorrow that a guardian could abandon him so utterly.

The artist adopted a familiar biblical tale and made it so vibrant and raw that its horrors appeared to unfold right in front of you

Viewing in front of the painting, observers recognize this as a real face, an precise depiction of a adolescent subject, because the identical youth – recognizable by his tousled locks and nearly black eyes – appears in two additional paintings by Caravaggio. In every instance, that highly expressive face dominates the scene. In John the Baptist, he gazes mischievously from the darkness while embracing a ram. In Victorious Cupid, he smirks with a hardness acquired on Rome's streets, his dark feathery appendages sinister, a unclothed child creating chaos in a well-to-do residence.

Amor Vincit Omnia, presently displayed at a London museum, constitutes one of the most discomfiting artworks ever created. Observers feel totally unsettled gazing at it. Cupid, whose arrows fill people with frequently agonizing longing, is portrayed as a extremely real, brightly lit unclothed form, straddling toppled-over items that comprise stringed devices, a music score, metal armor and an builder's T-square. This pile of possessions echoes, intentionally, the mathematical and architectural equipment strewn across the floor in Albrecht Dürer's print Melancholy – except in this case, the melancholic mess is caused by this grinning deity and the mayhem he can release.

"Love sees not with the vision, but with the soul, / And therefore is winged Love depicted sightless," penned the Bard, just before this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He gazes directly at the observer. That face – sardonic and ruddy-cheeked, staring with brazen assurance as he poses unclothed – is the same one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the same unusual-looking youth in the Eternal City at the start of the 17th century, he was the highly acclaimed religious artist in a city enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to adorn churches: he could adopt a biblical story that had been depicted many times previously and render it so new, so raw and physical that the terror appeared to be occurring immediately before you.

However there was a different side to the artist, apparent as quickly as he came in Rome in the cold season that concluded the sixteenth century, as a artist in his initial twenties with no teacher or supporter in the city, only skill and audacity. Most of the works with which he caught the holy city's attention were everything but holy. That could be the very earliest hangs in the UK's art museum. A youth parts his red lips in a yell of agony: while stretching out his filthy digits for a cherry, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's gloomy chamber mirrored in the cloudy liquid of the transparent container.

The adolescent wears a pink blossom in his coiffure – a symbol of the erotic trade in early modern painting. Northern Italian painters such as Tiziano and Palma Vecchio depicted prostitutes grasping blooms and, in a work lost in the second world war but known through images, Caravaggio represented a renowned woman prostitute, clutching a bouquet to her bosom. The message of all these floral indicators is obvious: sex for purchase.

What are we to make of Caravaggio's erotic depictions of youths – and of one adolescent in specific? It is a inquiry that has split his interpreters since he gained mega-fame in the twentieth century. The complicated past truth is that the artist was not the queer icon that, for example, Derek Jarman presented on screen in his twentieth-century movie Caravaggio, nor so entirely devout that, as some art scholars improbably assert, his Youth Holding Fruit is actually a likeness of Christ.

His initial works indeed offer explicit sexual suggestions, or including offers. It's as if Caravaggio, then a penniless youthful artist, aligned with Rome's sex workers, selling himself to survive. In the Florentine gallery, with this thought in consideration, viewers might turn to an additional initial creation, the sixteenth-century masterwork Bacchus, in which the deity of wine stares coolly at the spectator as he begins to untie the black sash of his robe.

A few annums after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was finally growing almost established with prestigious church commissions? This profane non-Christian god revives the erotic challenges of his initial paintings but in a increasingly intense, uneasy manner. Half a century afterwards, its hidden meaning seemed clear: it was a portrait of the painter's companion. A British visitor viewed Victorious Cupid in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] own youth or servant that laid with him". The name of this boy was Francesco.

The painter had been dead for about 40 years when this story was recorded.