What exactly was the black-winged deity of love? The secrets this masterwork reveals about the rebellious artist

A youthful boy cries out as his head is firmly held, a large thumb pressing into his cheek as his parent's powerful palm holds him by the throat. That scene from The Sacrifice of Isaac visits the Uffizi Gallery, evoking distress through Caravaggio's harrowing rendition of the tormented child from the biblical narrative. The painting appears as if Abraham, commanded by God to kill his offspring, could break his spinal column with a solitary turn. Yet Abraham's preferred method involves the silvery grey blade he grips in his other hand, ready to slit the boy's neck. One certain element remains – whomever posed as Isaac for this astonishing work displayed extraordinary acting ability. Within exists not just fear, surprise and pleading in his shadowed gaze but also deep sorrow that a guardian could betray him so utterly.

He adopted a well-known biblical story and transformed it so fresh and visceral that its horrors appeared to happen directly in front of you

Viewing in front of the painting, viewers recognize this as a real face, an precise record of a young subject, because the identical youth – recognizable by his disheveled locks and almost black pupils – appears in two other paintings by Caravaggio. In every case, that richly expressive visage commands the composition. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's streets, his dark plumed appendages demonic, a unclothed adolescent running chaos in a well-to-do residence.

Victorious Cupid, currently exhibited at a British museum, represents one of the most embarrassing artworks ever created. Observers feel completely unsettled looking at it. The god of love, whose arrows inspire people with frequently painful desire, is portrayed as a very real, brightly illuminated unclothed figure, standing over toppled-over items that include musical devices, a music score, plate armor and an architect's T-square. This heap of possessions resembles, deliberately, the geometric and architectural gear strewn across the floor in Albrecht Dürer's engraving Melencolia I – save in this case, the gloomy disorder is created by this smirking Cupid and the turmoil he can unleash.

"Love looks not with the eyes, but with the mind, / And therefore is winged Love painted sightless," penned the Bard, just prior to this painting was produced around 1601. But the painter's Cupid is not unseeing. He gazes straight at you. That countenance – ironic and rosy-cheeked, looking with brazen confidence as he struts naked – is the identical one that screams in fear in The Sacrifice of Isaac.

When the Italian master created his multiple portrayals of the same distinctive-looking youth in Rome at the dawn of the seventeenth century, he was the most acclaimed religious artist in a metropolis enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could adopt a scriptural story that had been depicted many times previously and render it so new, so unfiltered and visceral that the terror seemed to be happening directly before the spectator.

However there existed a different aspect to the artist, evident as soon as he came in Rome in the cold season that concluded the sixteenth century, as a artist in his initial twenties with no teacher or patron in the urban center, only skill and boldness. Most of the works with which he caught the holy metropolis's eye were everything but holy. What may be the absolute earliest hangs in the UK's art museum. A youth parts his red mouth in a yell of pain: while reaching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see the painter's gloomy room mirrored in the cloudy liquid of the transparent vase.

The adolescent sports a pink blossom in his hair – a symbol of the sex commerce in early modern art. Venetian artists such as Titian and Jacopo Palma portrayed prostitutes holding blooms and, in a painting lost in the WWII but known through images, the master represented a famous woman courtesan, clutching a bouquet to her bosom. The meaning of all these floral signifiers is clear: sex for sale.

What are we to make of Caravaggio's sensual depictions of youths – and of a particular adolescent in specific? It is a inquiry that has split his interpreters ever since he achieved mega-fame in the 1980s. The complicated past truth is that the painter was neither the queer icon that, for instance, Derek Jarman presented on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as certain artistic historians improbably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His early works do offer overt erotic implications, or even offers. It's as if Caravaggio, then a destitute youthful creator, aligned with Rome's sex workers, offering himself to survive. In the Uffizi, with this thought in mind, observers might turn to another initial creation, the sixteenth-century masterwork the god of wine, in which the deity of wine gazes coolly at the spectator as he starts to untie the dark ribbon of his robe.

A few annums following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally growing nearly respectable with important church commissions? This profane non-Christian deity resurrects the sexual challenges of his initial works but in a increasingly intense, uneasy way. Half a century later, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this boy was Cecco.

The artist had been dead for about forty annums when this account was recorded.