According to a story collected by the erudite Francesco Cancellieri in 1802, a pilgrim named "Stibeum" (from Latin: stibium, which means "antimony") was hosted in the villa for a night. That night, the pilgrim, identified later by some as the alchemist Giuseppe Francesco Borri—known as Giustiniano Bono—, searched the gardens of the villa overnight in search of a mysterious herb capable of concocting gold. Legend held that the next morning he was seen to disappear forever through a door, but left behind a few flakes of gold, the fruits of a successful alchemical transmutation, and a mysterious paper full of puzzling symbols and equations, putatively describing the ingredients and process required. The marquis had these symbols engraved on the five gates of the villa Palombara and on the walls of the mansion, hoping that one day they would be translated.
A second legend holds that between 1678 and 1680, the same Giuseppe Francesco Borri along with Athanasius Kircher and Gian Lorenzo Bernini designed and built the gate for the marquis. The marquis Palombara developed a passion for alchemy in 1656, when he visited the alchemical laboratory in Riario Palace, now known as Palazzo Corsini. Patronized by the exiled queen Christina of Sweden, the laboratory was supervised by Pietro Antonio Bandiera and had been visited by Borri and Kircher. This tradition holds the gate was built to memorialize a successful alchemical transmutation that occurred in the Riario Palace. It was rumored that Palombara, Bernini and Kircher were all poisoned on 28 November 1680, probably by Borri, for having revealed the secret formulas through the inscriptions on the gate.
Cancellieri published his semi-fanciful account in 1806, including his interpretation of the inscriptions on the Porta Alchimica. His work was published in June 1895 in French by Pietro Bornia as an issue of the periodical LInitiation'.