In 1191, on the death of his father Frederick Barbarossa, Henry VI assumed the title of Holy Roman Emperor and then King of Italy from the Pope. Immediately afterwards he moved to Sicily. Many cities of the Norman kingdom submitted, and only in Naples Henry VI found resistance. Two opposing factions are formed in Salerno: the one headed by Matteo d 'Aiello and his son Niccolò, bishop of the city, supported the old Altavillas, and the one headed by Archdeacon Arrigo, supporter of the Swabians.
The Swabian thread prevailed momentarily, in fact during the siege of Naples, the emperor fell ill and Salerno welcomed the sovereign to be treated by the doctors of his Medical School. Once Henry was cured he hurried back to Germany where, following the spread of the news of his death, riots had arisen. The Empress Constance of Altavilla instead stayed in Salerno in the palace of her ancestors, Castel Terracena.
The faction favorable to the Normans, in Salerno, led by Matteo d'Aiello, handed the Empress Constance into the hands of Tancredi. After a series of negotiations, the empress was released, but the betrayal of the Salerno people remained in the emperor's mind.
In 1194Henry VI returned to Italy and the insult suffered by his wife, sacking and destroying Salerno. The city was set on fire and many buildings were demolished. It was probably on this occasion that many of the School's manuscripts were brought to northern Europe where they are still preserved today. And this was certainly the moment that marked the beginning of the decline of the city.
Not even Henry VI's son, Frederick II, was tender with the former Norman capital. He issued several edicts which relegated Salerno to a secondary role. In particular, the Medical School lost part of its importance with the founding of the University in Naples, although in the Melfitane Constitutions Federico recognized the School as the exclusive authority to issue degrees in medicine.
With the reign of Manfredi, in 1254, the city experienced a revival. Salerno was able to count on a powerful ally, Giovanni da Procida, an adviser to the emperor from Salerno. In 1260, thanks also to him, work began to redevelop the port, strongly requested by the Salernitani; as evidence of this, even today, the oldest pier of the port bears the name of the Swabian ruler (molo Manfredi). Manfredi also founded the september San Matteo fair in 1259.