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A youthful boy screams as his head is firmly held, a massive digit pressing into his cheek as his father's mighty palm grasps 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 narrative. The painting seems as if Abraham, instructed by the Divine to sacrifice his son, could snap his spinal column with a solitary twist. However Abraham's preferred method involves the metallic grey knife he grips in his remaining hand, ready to slit Isaac's neck. One definite element stands out – whoever modeled as the sacrifice for this breathtaking work displayed extraordinary acting ability. There exists not just fear, shock and begging in his shadowed eyes but also profound grief that a guardian could abandon him so utterly.

He took a well-known scriptural story and made it so fresh and raw that its horrors appeared to happen right in view of you

Standing before the artwork, viewers recognize this as a real countenance, an accurate record of a young subject, because the identical boy – identifiable by his tousled hair and nearly dark pupils – features in several additional works by Caravaggio. In each case, that richly expressive visage dominates the scene. In Youth With a Ram, he peers playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black plumed wings demonic, a unclothed adolescent running chaos in a well-to-do residence.

Victorious Cupid, presently exhibited at a London museum, constitutes one of the most discomfiting artworks ever created. Observers feel totally disoriented gazing at it. The god of love, whose arrows inspire people with often painful longing, is shown as a extremely real, vividly illuminated unclothed form, straddling toppled-over items that include stringed instruments, a music manuscript, plate armour and an builder's ruler. This pile of items echoes, deliberately, the mathematical and construction equipment strewn across the floor in Albrecht Dürer's print Melancholy – save in this case, the melancholic mess is caused by this smirking deity and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And thus is winged Love depicted sightless," penned the Bard, shortly before this painting was produced around 1601. But the painter's Cupid is not blind. He gazes directly at the observer. That countenance – sardonic and rosy-cheeked, looking with bold confidence as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three images of the same unusual-appearing kid in Rome at the start of the 17th century, he was the highly celebrated religious painter in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could take a scriptural story that had been portrayed many occasions previously and make it so new, so raw and physical that the horror appeared to be occurring immediately in front of you.

However there existed another side to Caravaggio, apparent as quickly as he arrived in Rome in the cold season that ended 1592, as a artist in his early twenties with no mentor or patron in the urban center, just talent and boldness. The majority of the works with which he captured the holy metropolis's eye were everything but devout. That may be the absolute first hangs in the UK's art museum. A youth opens his red mouth in a scream of pain: while reaching out his dirty digits for a fruit, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can discern Caravaggio's dismal chamber reflected in the murky liquid of the glass container.

The adolescent sports a pink flower in his coiffure – a emblem of the erotic commerce in Renaissance art. Venetian painters such as Tiziano and Palma Vecchio portrayed courtesans holding blooms and, in a painting destroyed in the second world war but documented through images, the master represented a famous female courtesan, holding a posy to her bosom. The message of all these botanical indicators is clear: intimacy for purchase.

How are we to make of the artist's sensual depictions of youths – and of one adolescent in particular? It is a question that has split his commentators since he achieved mega-fame in the 1980s. The complex historical reality is that the painter was neither the homosexual hero that, for instance, the filmmaker put on screen in his 1986 movie Caravaggio, nor so entirely devout that, as certain art historians improbably assert, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial paintings do offer overt sexual suggestions, or including offers. It's as if the painter, then a destitute youthful artist, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in consideration, observers might look to another early creation, the sixteenth-century masterpiece Bacchus, in which the deity of wine stares calmly at the spectator as he starts to untie the dark sash of his robe.

A few years following the wine deity, what could have motivated the artist to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally growing nearly respectable with prestigious ecclesiastical commissions? This profane non-Christian god revives the sexual provocations of his initial works but in a more powerful, unsettling way. Half a century afterwards, its secret seemed obvious: it was a representation of the painter's companion. A British visitor saw the painting in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] own boy or servant that laid with him". The name of this adolescent was Cecco.

The painter had been dead for about forty years when this story was documented.