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A young boy cries out while his head is forcefully gripped, a large thumb digging into his face as his father's powerful palm holds him by the neck. That moment from Abraham's Sacrifice appears in the Florentine museum, evoking unease through Caravaggio's chilling rendition of the tormented child from the biblical narrative. The painting appears as if the patriarch, commanded by the Divine to sacrifice his son, could break his spinal column with a single turn. Yet Abraham's chosen approach involves the metallic grey blade he holds in his other palm, ready to slit Isaac's neck. A certain element stands out – whoever posed as the sacrifice for this breathtaking piece displayed extraordinary expressive ability. Within exists not just fear, surprise and pleading in his darkened eyes but also deep grief that a guardian could abandon him so completely.

He adopted a well-known biblical story and transformed it so fresh and raw that its terrors appeared to unfold right in view of the viewer

Standing in front of the artwork, viewers identify this as a actual face, an accurate depiction of a adolescent model, because the identical boy – identifiable by his disheveled locks and almost black eyes – features in several other paintings by Caravaggio. In every instance, that highly expressive visage commands the composition. In John the Baptist, he peers playfully from the shadows while holding a ram. In Victorious Cupid, he grins with a toughness learned on the city's streets, his black feathery appendages sinister, a naked adolescent creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most discomfiting artworks ever painted. Observers feel completely unsettled gazing at it. The god of love, whose arrows fill people with often painful desire, is portrayed as a very real, vividly illuminated nude figure, straddling overturned objects that include stringed devices, a musical score, metal armor and an architect's ruler. This pile of possessions echoes, intentionally, the mathematical and construction equipment scattered across the ground in the German master's engraving Melancholy – except in this case, the gloomy disorder is created by this grinning deity and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And therefore is feathered Love depicted sightless," penned the Bard, shortly before this painting was produced around the early 1600s. But Caravaggio's Cupid is not blind. He gazes directly at the observer. That face – ironic and rosy-faced, staring with brazen confidence as he poses unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his three portrayals of the identical unusual-appearing kid in the Eternal City at the start of the 17th century, he was the most celebrated religious painter in a metropolis ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a biblical story that had been portrayed many occasions previously and make it so new, so unfiltered and visceral that the terror appeared to be occurring immediately in front of the spectator.

However there existed another aspect to Caravaggio, apparent as quickly as he arrived in Rome in the winter that ended the sixteenth century, as a artist in his early twenties with no mentor or patron in the urban center, only talent and boldness. The majority of the works with which he caught the holy metropolis's attention were everything but holy. What could be the absolute earliest resides in the UK's art museum. A young man opens his red mouth in a scream of pain: while stretching out his dirty fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern Caravaggio's dismal chamber reflected in the cloudy waters of the glass vase.

The boy sports a rose-colored flower in his coiffure – a symbol of the erotic trade in Renaissance painting. Northern Italian painters such as Titian and Jacopo Palma depicted prostitutes grasping blooms and, in a painting lost in the second world war but documented through photographs, Caravaggio represented a renowned female prostitute, holding a posy to her bosom. The message of all these floral indicators is clear: intimacy for sale.

What are we to make of the artist's erotic portrayals of boys – and of a particular boy in specific? It is a inquiry that has divided his interpreters ever since he gained mega-fame in the twentieth century. The complicated past reality is that the painter was not the homosexual icon that, for example, Derek Jarman put on film in his 1986 film about the artist, nor so completely pious that, as some art historians improbably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His initial paintings indeed offer explicit erotic implications, or even propositions. It's as if Caravaggio, then a penniless youthful creator, aligned with the city's sex workers, selling himself to survive. In the Uffizi, with this idea in consideration, observers might turn to an additional initial creation, the sixteenth-century masterwork Bacchus, in which the god of alcohol stares coolly at the spectator as he starts to undo the dark ribbon of his garment.

A several years after the wine deity, what could have driven Caravaggio to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing almost respectable with prestigious ecclesiastical commissions? This profane non-Christian god revives the erotic challenges of his early works but in a more intense, unsettling manner. Half a century later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A British visitor saw Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth 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.