What was the dark-feathered god of love? The insights this masterwork reveals about the rogue artist

The youthful lad cries out while his skull is firmly held, a massive digit pressing into his face as his father's powerful palm grasps him by the throat. That moment from Abraham's Sacrifice appears in the Florentine museum, evoking distress through Caravaggio's harrowing portrayal of the suffering youth from the biblical account. The painting appears as if the patriarch, instructed by the Divine to kill his offspring, could break his spinal column with a single twist. However the father's preferred approach involves the silvery steel knife he holds in his other hand, ready to slit Isaac's neck. A definite aspect stands out – whoever posed as the sacrifice for this breathtaking work demonstrated extraordinary acting skill. Within exists not only fear, shock and begging in his shadowed gaze but also profound grief that a guardian could betray him so completely.

He took a familiar scriptural story and transformed it so fresh and raw that its horrors appeared to unfold directly in view of you

Standing in front of the painting, viewers identify this as a real face, an precise record of a adolescent model, because the same boy – identifiable by his tousled hair and almost black pupils – features in two additional works by the master. In every instance, that highly emotional face dominates the composition. In Youth With a Ram, he peers playfully from the darkness while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his dark feathery appendages demonic, a unclothed child creating riot in a affluent dwelling.

Victorious Cupid, currently displayed at a British museum, represents one of the most discomfiting artworks ever created. Observers feel completely disoriented looking at it. Cupid, whose arrows fill people with frequently agonizing desire, is portrayed as a very real, vividly illuminated nude form, straddling toppled-over items that include stringed devices, a music score, metal armor and an builder's ruler. This pile of items resembles, deliberately, the geometric and construction equipment strewn across the floor in Albrecht Dürer's engraving Melancholy – except in this case, the melancholic disorder is caused by this smirking Cupid and the turmoil he can release.

"Love looks not with the eyes, but with the mind, / And therefore is feathered Cupid painted blind," penned Shakespeare, shortly prior to this painting was created around the early 1600s. But the painter's Cupid is not blind. He gazes directly at the observer. That face – ironic and ruddy-cheeked, looking with brazen confidence as he struts unclothed – is the identical one that shrieks in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-looking kid in the Eternal City at the dawn of the 17th century, he was the most celebrated sacred artist in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn churches: he could adopt a scriptural story that had been depicted many occasions before and render it so new, so unfiltered and visceral that the terror seemed to be occurring directly before the spectator.

However there existed a different side to the artist, evident as quickly as he arrived in the capital in the winter that concluded 1592, as a painter in his initial 20s with no mentor or supporter in the city, just talent and boldness. The majority of the paintings with which he caught the holy metropolis's attention were everything but devout. What may be the very first hangs in London's art museum. A young man parts his crimson mouth in a yell of agony: while stretching out his dirty digits for a cherry, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can discern Caravaggio's dismal room reflected in the cloudy liquid of the glass container.

The adolescent wears a pink flower in his coiffure – a emblem of the erotic trade in Renaissance art. Venetian painters such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a painting lost in the WWII but documented through images, the master represented a renowned female courtesan, holding a bouquet to her chest. The message of all these floral indicators is obvious: intimacy for sale.

What are we to make of the artist's sensual depictions of youths – and of one adolescent in specific? It is a question that has split his interpreters since he gained mega-fame in the 1980s. The complicated historical truth is that the artist was neither the homosexual hero that, for example, Derek Jarman put on screen in his twentieth-century film about the artist, nor so entirely pious that, as certain art scholars unbelievably claim, his Youth Holding Fruit is actually a portrait of Christ.

His initial works do offer overt erotic suggestions, or even propositions. It's as if the painter, then a penniless youthful artist, identified with Rome's sex workers, selling himself to survive. In the Uffizi, with this thought in mind, observers might turn to another early work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at you as he starts to undo the dark ribbon of his robe.

A few years after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was finally growing nearly respectable with important ecclesiastical commissions? This profane non-Christian god revives the sexual challenges of his initial paintings but in a more powerful, unsettling way. Half a century later, its secret seemed clear: it was a portrait of Caravaggio's lover. A English traveller viewed Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Francesco.

The artist had been dead for about 40 years when this account was documented.