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A youthful lad screams as his skull is firmly held, a large digit digging into his face as his father's mighty hand holds him by the neck. This moment 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, instructed by God to kill his son, could snap his neck with a single twist. However the father's chosen approach involves the metallic steel blade he grips in his remaining palm, ready to cut the boy's neck. A certain element stands out – whomever modeled as Isaac for this breathtaking work displayed extraordinary expressive ability. There exists not just fear, surprise and begging in his darkened eyes but additionally profound grief that a protector could abandon him so utterly.

He adopted a familiar scriptural story and made it so fresh and raw that its terrors appeared to unfold directly in front of the viewer

Viewing in front of the painting, observers identify this as a real face, an precise depiction of a young subject, because the same boy – identifiable by his tousled locks and nearly black pupils – features in two other paintings by Caravaggio. In every case, that richly expressive face commands the composition. In John the Baptist, he gazes playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on the city's alleys, his dark plumed wings sinister, a naked child running riot in a affluent dwelling.

Amor Vincit Omnia, presently displayed at a London gallery, constitutes one of the most discomfiting artworks ever created. Viewers feel completely disoriented looking at it. Cupid, whose arrows fill people with frequently agonizing desire, is portrayed as a extremely tangible, vividly lit nude form, straddling overturned items that comprise musical instruments, a music manuscript, metal armour and an builder's T-square. This pile of possessions echoes, intentionally, the geometric and architectural equipment strewn across the ground in the German master's print Melancholy – except in this case, the gloomy disorder is created by this grinning Cupid and the turmoil he can release.

"Love looks not with the eyes, but with the soul, / And therefore is winged Love depicted blind," wrote the Bard, just prior to this painting was created around the early 1600s. But Caravaggio's Cupid is not blind. He stares straight at you. That face – sardonic and rosy-faced, looking with brazen assurance as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

When the Italian master painted his multiple images of the same unusual-looking kid in Rome at the start of the 17th century, he was the most celebrated religious painter in a metropolis enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted numerous occasions before and render it so new, so unfiltered and physical that the terror seemed to be occurring directly before you.

However there was a different aspect to Caravaggio, apparent as soon as he came in Rome in the winter that concluded 1592, as a painter in his initial 20s with no mentor or patron in the urban center, just talent and audacity. Most of the works with which he caught the holy city's eye were everything but devout. What may be the absolute earliest resides in London's National Gallery. A youth parts his red lips in a yell of pain: while stretching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: observers can see Caravaggio's gloomy chamber reflected in the murky waters of the transparent vase.

The boy sports a pink flower in his coiffure – a emblem of the sex trade in early modern art. Venetian painters such as Titian and Palma Vecchio depicted prostitutes grasping blooms and, in a work lost in the second world war but known through photographs, the master represented a renowned female courtesan, clutching a posy to her bosom. The message of all these floral indicators is clear: sex for purchase.

What are we to interpret of Caravaggio's sensual portrayals of youths – and of one adolescent in particular? It is a question that has divided his commentators since he achieved widespread recognition in the 1980s. The complex past reality is that the artist was neither the queer icon that, for example, the filmmaker presented on screen in his twentieth-century movie about the artist, nor so completely pious that, as some artistic scholars improbably assert, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His initial works indeed offer overt erotic suggestions, or including offers. It's as if Caravaggio, then a destitute young artist, identified with Rome's sex workers, selling himself to survive. In the Florentine gallery, with this idea in mind, observers might look to an additional initial work, the 1596 masterpiece the god of wine, in which the god of alcohol stares coolly at the spectator as he starts to untie the black ribbon of his garment.

A several years following Bacchus, what could have driven Caravaggio to create Victorious Cupid for the art patron the nobleman, when he was at last becoming nearly respectable with important ecclesiastical projects? This profane non-Christian god revives the sexual provocations of his early paintings but in a more powerful, uneasy manner. Fifty years 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 informed its subject has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this boy was Francesco.

The painter had been dead for about 40 annums when this account was recorded.