The Czar received dignitaries of the Order in St. Petersburg on 10 September 1798 and proclaimed his decision to keep the institutions, privileges and honours of the Order of Saint John intact. On 3 October 1798 the Priory of Poland associated itself to the vote, followed by the Priory of Germany twenty days later. Both of these priories accepted the proclamation of 10 September regarding the establishment of the Order in St. Petersburg. However, the members of the French Priory had been dispersed upon the suppression of the Order in France and therefore could not entirely adhere to the proclamation.
On 27 October 1798, at the urging of Pope Pius VI, the Knights present in St. Petersburg, together with those of the Grand Priory of Russia, the Priory of Germany and that of Poland, elected His Imperial Majesty Czar Paul I as 70th Grand Master of the Order of Saint John of Jerusalem. The czar accepted on the 13 November 1798, instituting the Hereditary Commandries of the Order in Russia composed of two Grand Priories (one Catholic and one Orthodox). These were made up of 249 Knights of different classes, ranks, and nationalities (Ukase n. 19044).
In the meantime, von Hompesch had escaped from Malta and taken refuge in Trieste with sixteen Knights. On 6 July 1799, he was forced to acknowledge the abdication act and submitted to the role of the Russian Emperor, the 70th Grand Master of the Order.
The nomination of the Czar is to be noted in order to prove his legitimacy. Not only did von Hompesch accept (despite the fact that this was not juridically necessary), so did the other Grand Priories and Pius VI as Head of the Church. This he did by issuing a Papal Bull on 10 June 1799 (“Pastoralium nobis”) in order to contrast the growing power of Napoleon. This being the case, the claims subsequently made by those who question the validity of the Czar’s election are discredited.
The Order had in the meantime received many more important acknowledgements. In 1794, the future president of the United States, James Monroe, signed a treaty of alliance between his nation and the Order.
After the death of the Czar his son Alexander I confirmed the protection of the Order by the Imperial Family (16 March 1801: “ … wanting to give proof of our special good will and affection for the Sovereign Order of Saint John of Jerusalem, I will do whatever is in my power to ensure that the Order maintains its rights, honours, privileges and property…”). He did not however assume direct role as Grand Master for political reasons. Instead, he installed Field-Marshall Count Nicholas Soltykoff as Lieutenant Grand Master on 16 March 1801, expecting that the Knights would once again be in possession of the islands of Malta, as would also be established in the Treaty of Amiens on 25 March 1802.