Who was Caravaggio's dark-feathered god of desire? What insights that masterwork uncovers about the rogue genius

A young boy screams as his head is firmly gripped, a large digit pressing into his face as his father's powerful hand grasps him by the throat. That moment from Abraham's Sacrifice visits the Florentine museum, creating unease through the artist's chilling rendition of the tormented child from the scriptural narrative. The painting seems as if Abraham, instructed by the Divine to kill his son, could break his spinal column with a single twist. Yet Abraham's preferred method involves the metallic grey knife he grips in his remaining hand, prepared to slit the boy's neck. One definite element remains – whomever modeled as the sacrifice for this astonishing work demonstrated remarkable acting ability. Within exists not only fear, surprise and begging in his darkened gaze but additionally deep grief that a protector could abandon him so completely.

He took a familiar biblical story and transformed it so vibrant and visceral that its horrors seemed to unfold directly in view of you

Standing in front of the artwork, viewers identify this as a real countenance, an accurate record of a young subject, because the same youth – recognizable by his tousled locks and almost black pupils – features in several additional paintings by the master. In every instance, that richly expressive visage commands the composition. In John the Baptist, he gazes playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a hardness learned on the city's streets, his dark feathery wings sinister, a unclothed adolescent creating chaos in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a British gallery, represents one of the most discomfiting artworks ever created. Observers feel totally disoriented looking at it. Cupid, whose arrows fill people with often agonizing desire, is shown as a very tangible, vividly lit unclothed form, standing over overturned objects that comprise stringed instruments, a musical manuscript, plate armour and an builder's T-square. This pile of items echoes, intentionally, the geometric and architectural gear scattered across the ground in the German master's engraving Melancholy – save in this case, the gloomy disorder is created by this grinning deity and the turmoil he can release.

"Love sees not with the eyes, but with the soul, / And therefore is feathered Love painted blind," wrote Shakespeare, just before this painting was created around the early 1600s. But Caravaggio's god is not blind. He gazes straight at the observer. That countenance – ironic and rosy-cheeked, looking with brazen assurance as he struts unclothed – is the same one that shrieks in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his multiple portrayals of the same unusual-looking kid in the Eternal City at the dawn of the seventeenth century, he was the highly celebrated religious painter in a city enflamed by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn sanctuaries: he could take a scriptural story that had been depicted numerous times previously and render it so new, so raw and physical that the horror seemed to be occurring directly in front of the spectator.

However there existed a different aspect to the artist, evident as soon as he arrived in the capital in the cold season that concluded the sixteenth century, as a painter in his initial 20s with no teacher or supporter in the urban center, only skill and audacity. The majority of the works with which he caught the holy city's eye were anything but devout. That may be the absolute earliest resides in London's National Gallery. A young man parts his red lips in a yell of agony: while stretching out his dirty fingers for a fruit, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern the painter's dismal chamber reflected in the murky waters of the glass vase.

The adolescent wears a rose-colored blossom in his coiffure – a symbol of the erotic commerce in early modern painting. Venetian painters such as Titian and Palma Vecchio depicted courtesans grasping blooms and, in a painting destroyed in the WWII but documented through images, the master portrayed a famous woman prostitute, holding a bouquet to her chest. 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 boy in particular? It is a question that has divided his commentators ever since he achieved widespread recognition in the 1980s. The complicated past reality is that the painter was not the queer hero that, for example, the filmmaker put on film in his twentieth-century film about the artist, nor so completely pious that, as some artistic scholars unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early paintings do offer overt sexual suggestions, or including propositions. It's as if the painter, then a destitute young artist, identified with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in consideration, viewers might turn to another early work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at the spectator as he begins to undo the black sash of his robe.

A several years following Bacchus, what could have driven Caravaggio to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was finally growing almost respectable with prestigious church commissions? This unholy non-Christian deity resurrects the sexual provocations of his initial paintings but in a more intense, uneasy manner. Half a century later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's companion. A English traveller saw the painting in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own boy or assistant that slept with him". The name of this adolescent was Cecco.

The painter had been deceased for about 40 annums when this account was documented.