In 1800, Lopukhin and Senator Spiridonov completed a three-year senatorial inspection of the provinces of Kazan, Viatka and Orenburg, in which they identified various abuses of power by the local administrations. In his report to the Tsar, Lopukhin displayed particular consideration for the peasantry.

The following year, in 1801, Tsar Alexander I ordered Lopukhin and Senator Neledinskiy-Meletskiy to undertake a senatorial inspection of the provinces of south Russia to study the status of sectarian religion in the region, and in particular, to investigate a series of complaints by Doukhobors, who had returned there from exile, about their living conditions.

Arriving in Kharkov in November 1801, Lopukhin met with the Governor and requested records relating to the history of the Doukhobors in the province. Lopukhin learned that during Catherine the Great’s reign, “several” local Doukhobors were summarily imprisoned and “not returned”. Under Tsar Paul, entire Doukhobor households were exiled into penal servitude. In August 1801, however, the exiled sectarians were returned to their former homes in Kharkov province following Tsar Alexander’s edict of release.

Lopukhin was alarmed by the haste with which local authorities began “admonishing” the returning Doukhobors. He bluntly told the Governor that rebellion would surely ensue; the sectarians “did not have time to rest quietly” before they were accosted by civil and ecclesiastical officials. Lopukhin ordered the Governor to recall the “teams” sent to the districts to “counsel” the Doukhobors.

The next day, however, the Governor, “pale, with papers in hand,” rushed to Lopukhin’s lodgings with news that a bunt (rebellion) had already broken out among the Doukhobors of Izium district “where an admonition was performed.” The worried Governor informed Lopukhin that the sectarians, several of whom had already been arrested, renounced recognition of the Tsar and Jesus Christ and vowed never to pay taxes nor fulfill state obligations. The Izium land court was investigating the incident.

Lopukhin calmed the Governor by assuring him that the “rebellion” would be subdued and others prevented. The problem, as Lopukhin saw it, was that the interrogations of the Doukhobors were “needless” and “unskilled”; they served only to embitter them. The Senator defended the sectarians, remonstrating that they were “full of reverence” toward Jesus Christ and the Tsar and ready to “obey all laws” and “fulfill all land obligations”. To alleviate the situation, Lopukhin ordered the Governor to release the arrested Doukhobors and suspend the inquiry. The Governor agreed.

Lopukhin wrote a report of his investigation to the Tsar dated November 12, 1801. The Tsar was informed that the Kharkov authorities did not understand the “direct essence” of his edicts concerning the Doukhobors, that the “rebellion” was not the fault of the sectarians themselves, who displayed “faith and reverence” and “particular gratitude” towards the monarch. The Senator outlined the remedial measures he had ordered the Kharkov Governor to adopt.

During the course of his investigation, Lopukhin met for a period of several days with a sizeable group of Doukhobors. This was done in secrecy so as not to arouse “unnecessary inquisitiveness” among the Orthodox. He was impressed by the sectarians’ faith and “very fundamental and correct concepts of Christianity” and sympathized with their plight. For their part, the Doukhobors “took a liking” to Lopukhin, and they conversed openly with him about the tenets of their faith. On the last day of their meetings, the Doukhobors presented a petition to Lopukhin requesting to be established “in a separate colony” and expressing their “loyalty and real zeal toward the sovereign”.

Lopukhin wrote a second report to the Tsar, skillfully rendering the Doukhobors request. It began with a hearty defense of the sectarians in the face of unfavourable reports issued by Kharkov officials. The Senator then offered a short explanation of the Doukhobor “manner of faith”. Finally, Lopukhin relayed their request for a separate colony, using language that consciously echoed Alexander’s emphasis on legal treatment for non-conformists and his desire to lead them back to Orthodoxy. First, Lopukhin argued that the formation of a separate colony would quiet Doukhobor unrest by removing them from the harassment and animosity of local officials. Second, isolation would all but eliminate the sectarians’ ability to spread their beliefs. Finally, concentrated settlements would help well-educated, moral and patient priests bring the Doukhobors back to Orthodoxy.

The Tsar agreed wholeheartedly with Lopukhin’s proposal and immediately set in motion the consolidation of a separate Doukhobor colony in the recently incorporated lands of Novorossiya. In his January 1802 edict, the Tsar granted permission for any Doukhobor in the Novorossiya provinces to settle together in the Molochnye Vody region of Melitopol district, Tavria province, which was then a sparsely populated part of the empire. Alexander wrote to the Governor of Novorossiya that the concentration of Doukhobors, separate from other Russians, would prevent their further ruin and mistreatment, and that he considered their separation to be “a most reliable means for the extinguishing of their heresay and for the suppression of their influence on others.”  In the years that followed, the Tsar extended the edict to allow Doukhobors from across the Russian Empire to resettle in Tavria.

Lopukhin's involvement in the "Doukhobor Affair" would determine the fate of the sect throughout Russia for the next forty years. For the first time, the Doukhobors had in Lopukhin a sympathetic high official who spoke up for the sectarians and stressed their virtues as well as their faults.  He acted as a conduit between the Doukhobors and the highest circles of Russian society, transmitting their beliefs using the language and metaphors of the Imperial Court, and in doing so, helped lay the basis for Tsar Alexander's policy on the Doukhobors.  But for his intervention, the Doukhobors of Sloboda-Ukraine and elsewhere would have remained isolated, dispersed, voiceless and oppressed.  It is through his efforts that the Doukhobors owed a great measure of release from persecution, and also an opportunity to exist and develop as a self-contained community. 

Lopukhin left Kharkov in December of 1801 to resume his senatorial duties.  Between 1802 and 1805, he served as President of a commission "to deal with the dispute of estates in the Crimea", travelling to the Crimea to the Crimea to settle land disputes between Tatars and Russian landlords.  In 1806, he observed the formation of national armed forces in Vladimir, Kaluga, Ryazan and Tula provinces.  In 1807, he served in the Eight Department of the Senate, a branch of the Senate which was located in Moscow. 

In 1808-1809, the “Zapiska Niekotorykh Obstoiatel’stv Zhizni i Sluzhby Dieistvitel’nago Tainago Sovietnika, Senatora I. V. Lopukhina” ["A note on some circumstances in the life and career of Acting Privy Councillor, Senator I. V. Lopukhin"] was written under Lopukhin's dictation.  The tract contained Lopukhin's detailed reminisces on the "Doukhobor Affair".

In 1812, during the Napoleonic War, Lopukhin fled Moscow to escape the advancing French armies, resettling to his estate of Saviiskoye in the Baltic. In 1813, Lopukhin took a leave of absence from the Senate for health reasons, which was repeatedly prolonged.  He moved back to his family estate at Voskresenskoye and married the daughter of Moscow merchant M.E. Nikitin.  From 1814 until the end of his life, Lopukhin was a member of the Russian Bible Society, a non-denominational organization devoted to translating and distributing the Bible in Russia. 

Throughout his later career and until his death, Lopukhin was censured by Orthodox clergy, local and provincial officials, and by conservative elements within the Russian aristocracy for his efforts on behalf of the Doukhobors.  The Senator ignored the criticism until the Holy Synod (council of Orthodox bishops of the Russian Empire) reproached him for the “harmful multiplication” of Doukhobors. In response to his critics, Lopukhin composed the essay "Glas Iskrennosti" ["Voice of Sincerity"], explaining the Doukhobors' "errors of faith", outlining their history of persecution, and defending his activities in connection with the sect. The essay was circulated privately in 1806, but was only published posthumously in 1817.

In addition to 'Glas Iskrennosti', there are several historical tracts on the Doukhobors attributed to Lopukhin. The first of these, "Zapiska, Rodannaya Dukhobortsami Ekaterinoslavskoy Gubernii v 1791 g. Gubernatoru Kakhovskomu" ["Note of 1791 submitted by the Doukhobors of Ekaterinoslav Province to Governor Kakhovsky"] contains one of the earliest expositions of Dukhobor beliefs. The Note is known only in copies; the original has never been discovered.  However, scholars have ascertained that the first copy was made from a document belonging to Lopukhin.  The second tract is an 1805 note entitled "Nekotorye Cherty ob Obshchestve Dukhobortsev" ["Several Characteristics of Doukhobor Society"]. While the authorship of these tracts has not been positively identified, scholars such as Svetlana Inikova have identified Masonic influences in both, and have justifiably attributed them to either an unidentified Mason or directly to Lopukhin himself. 

Lopukhin died at his family estate on 22 June 1816.  Among his contemporaries, he enjoyed great popularity as the epitome of the fair and disinterested judge, the philanthropist, the man who put the welfare of his Motherland before his own, the trusted advisor to the Tsars.  At the same time, his mystic writings and philosophy earned him many denigrators who accused him of hypocrisy and personal defects.  Sadly, his role and influence in the history of the Doukhobors, perhaps second only to Tolstoy amongst "outsiders" to the sect, remains largely unappreciated and forgotten.

For more about Lopukhin's legacy as a writer and thinker see: Lipski, Alexander. "A Russian Mystic Faces the Age of Rationalism and Revolution: Thought and Activity of Ivan Vladimirovich Lopukhin" in Church History (Vol. 36, No. 2 (Jun., 1967), pp. 170-188; and Billington, James H. "The Icon and the Axe, An Interpretive History of Russian Culture" (New York: Random House, 1966.

For more about Lopukhin's investigation of the Sloboda-Ukraine Doukhobors and the formation of the Milky Waters colony see: Fry, Gary Dean. "The Doukhobors, 1801-1855: Origins of a Successful Dissident Sect" (Ph.D thesis, American University, 1976); and Savva, Vladimir Ivanovich, “K Istorii Dukhobortsev Khar’kovskoi Gubernii” (Kharkov, Kharkov Historical-Philological Society, 1893); republished in P.N. Malov, “Dukhobortsi, ikh Istoria, Zhizn' i Bor'ba”; translated as More about the History of the Dukhobortsy of Kharkov Province on the Doukhobor Genealogy Website.