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A young boy cries out while his head is forcefully held, a large thumb pressing into his cheek as his father's powerful hand holds him by the neck. This scene from The Sacrifice of Isaac visits the Florentine museum, evoking unease through Caravaggio's harrowing rendition of the tormented youth from the biblical narrative. The painting seems as if the patriarch, commanded by the Divine to sacrifice his offspring, could snap his spinal column with a single turn. Yet Abraham's preferred approach involves the silvery grey blade he grips in his other hand, prepared to slit Isaac's throat. A definite aspect stands out – whomever posed as Isaac for this breathtaking work displayed extraordinary acting ability. There exists not only dread, surprise and pleading in his shadowed eyes but also profound sorrow that a guardian could betray him so completely.

He adopted a well-known scriptural 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 actual countenance, an accurate record of a young model, because the same boy – identifiable by his disheveled hair and nearly black eyes – appears in several other paintings by the master. In every case, that highly expressive face commands the composition. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black plumed wings sinister, a naked child running riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most embarrassing masterpieces ever created. Viewers feel totally disoriented looking at it. Cupid, whose arrows inspire people with often painful desire, is portrayed as a extremely tangible, vividly illuminated nude form, standing over overturned items that include stringed instruments, a musical score, metal armour and an builder's T-square. This pile of items resembles, deliberately, the mathematical and construction equipment scattered across the ground in the German master's engraving Melencolia I – save in this case, the gloomy disorder is caused by this grinning Cupid and the mayhem he can unleash.

"Affection looks not with the eyes, but with the mind, / And thus is feathered Cupid painted blind," wrote the Bard, just before this painting was produced around the early 1600s. But the painter's god is not blind. He stares directly at you. That face – ironic and ruddy-cheeked, looking with bold confidence as he poses unclothed – is the identical one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three portrayals of the identical distinctive-looking kid in Rome at the start of the seventeenth century, he was the most acclaimed sacred painter in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was sought to decorate sanctuaries: he could adopt a biblical narrative that had been depicted many times previously and make it so fresh, so raw and visceral that the terror appeared to be occurring directly in front of the spectator.

However there existed a different side to the artist, evident as quickly as he arrived in Rome in the cold season that ended the sixteenth century, as a painter in his early 20s with no teacher or patron in the city, only talent and audacity. The majority of the works with which he captured the holy city's attention were anything but devout. That could be the absolute first hangs in London's National Gallery. A youth opens his crimson lips in a yell of pain: while stretching out his dirty fingers for a fruit, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern Caravaggio's dismal chamber reflected in the cloudy liquid of the transparent container.

The boy wears a rose-colored blossom in his hair – a symbol of the erotic trade in Renaissance art. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes holding blooms and, in a painting destroyed in the second world war but known through images, the master portrayed a famous female prostitute, clutching a posy to her bosom. The meaning of all these botanical indicators is clear: intimacy for purchase.

What are we to interpret of Caravaggio's sensual depictions of boys – and of one adolescent in specific? It is a inquiry that has divided his interpreters since he gained mega-fame in the 1980s. The complicated historical reality is that the artist was not the homosexual hero that, for instance, Derek Jarman presented on film in his twentieth-century film Caravaggio, nor so entirely pious that, as certain artistic scholars improbably assert, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His initial works indeed offer overt sexual suggestions, or even propositions. It's as if Caravaggio, then a destitute young artist, aligned with Rome's prostitutes, selling himself to survive. In the Florentine gallery, with this idea in consideration, viewers might look to another initial work, the sixteenth-century masterwork Bacchus, in which the deity of alcohol stares calmly at you as he starts to untie the dark ribbon of his garment.

A few years after the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally growing almost established with prestigious church commissions? This unholy non-Christian god resurrects the sexual challenges of his initial works but in a more intense, unsettling way. Fifty years afterwards, its secret seemed obvious: it was a portrait of the painter's lover. A British visitor saw the painting in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or servant that laid with him". The name of this adolescent was Cecco.

The artist had been deceased for about 40 years when this story was recorded.