Who exactly was Caravaggio's dark-feathered deity of desire? What secrets this masterpiece uncovers about the rogue artist

The youthful boy screams as his head is firmly gripped, a massive digit pressing into his cheek as his parent's mighty palm holds him by the neck. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through the artist's harrowing rendition of the tormented child from the scriptural narrative. It appears as if the patriarch, commanded by God to sacrifice his offspring, could break his neck with a solitary turn. However Abraham's preferred approach involves the metallic steel knife he holds in his other hand, ready to slit the boy's throat. One definite element remains – whoever modeled as Isaac for this breathtaking work demonstrated extraordinary acting skill. Within exists not only dread, surprise and begging in his darkened gaze but additionally deep sorrow that a protector could betray him so utterly.

He adopted a well-known biblical tale and transformed it so vibrant and visceral that its horrors seemed to unfold right in front of you

Standing before the painting, viewers identify this as a real countenance, an precise depiction of a adolescent subject, because the same boy – identifiable by his disheveled hair and almost black eyes – appears in several additional paintings by Caravaggio. In every instance, that richly emotional visage dominates the composition. In John the Baptist, he peers mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a toughness learned on the city's alleys, his black plumed wings demonic, a unclothed adolescent running riot in a well-to-do residence.

Amor Vincit Omnia, presently displayed at a British museum, constitutes one of the most embarrassing masterpieces ever painted. Viewers feel completely unsettled gazing at it. The god of love, whose darts fill people with frequently painful longing, is portrayed as a extremely tangible, brightly lit unclothed form, standing over overturned objects that include musical instruments, a musical manuscript, plate armour and an builder's ruler. This pile of items resembles, deliberately, the mathematical and construction gear scattered across the floor in the German master's print Melencolia I – except in this case, the gloomy mess is caused by this grinning Cupid and the turmoil he can unleash.

"Affection sees not with the eyes, but with the mind, / And therefore is winged Love painted sightless," wrote the Bard, just prior to this work was produced around 1601. But Caravaggio's Cupid is not blind. He stares straight at the observer. That countenance – sardonic and ruddy-cheeked, staring with brazen confidence as he poses naked – is the identical one that screams in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three images of the identical unusual-appearing kid in Rome at the start of the 17th century, he was the highly acclaimed sacred painter in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could take a biblical narrative that had been depicted numerous times before and make it so new, so unfiltered and physical that the horror seemed to be happening directly in front of you.

Yet there was another aspect to Caravaggio, evident as soon as he came in Rome in the cold season that ended 1592, as a painter in his initial 20s with no teacher or patron in the city, only skill and boldness. Most of the works with which he caught the sacred city's attention were everything but holy. That may be the very first hangs in the UK's National Gallery. A youth parts his red mouth in a scream of pain: while stretching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern the painter's gloomy chamber mirrored in the murky waters of the glass container.

The adolescent wears a rose-colored blossom in his coiffure – a symbol of the erotic trade in early modern painting. Northern Italian artists such as Titian and Jacopo Palma portrayed prostitutes grasping blooms and, in a work destroyed in the second world war but known through images, the master represented a renowned woman courtesan, clutching a posy to her chest. The message of all these floral indicators is obvious: sex for purchase.

What are we to make of Caravaggio's erotic depictions of boys – and of one adolescent in particular? It is a question that has divided his interpreters since he gained mega-fame in the 1980s. The complicated past reality is that the artist was neither the queer icon that, for instance, the filmmaker put on film in his 1986 film about the artist, nor so completely devout that, as some artistic historians improbably assert, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early works indeed make explicit erotic suggestions, or even offers. It's as if the painter, then a destitute youthful creator, aligned with Rome's sex workers, selling himself to live. In the Florentine gallery, with this idea in consideration, viewers might look to another early creation, the sixteenth-century masterwork the god of wine, in which the god of alcohol stares calmly at the spectator as he begins to undo the black sash of his garment.

A few annums following the wine deity, what could have motivated Caravaggio to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally growing nearly established with prestigious ecclesiastical projects? This unholy non-Christian deity resurrects the erotic challenges of his early works but in a increasingly powerful, uneasy manner. Half a century afterwards, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British visitor saw Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The name of this adolescent was Francesco.

The painter had been dead for about forty annums when this story was recorded.