Returning to live among the monks of Neamț, Vârnav involved himself in the controversy over the secularization of monastery estates.
Moldavia's Education Minister, Alexandru Teriachiu, assigned him to a reform committee which uncovered great irregularities at Neamț, including a dysfunctional seminary and an inhumane ward for the insane.
Vârnav refurbished the seminary, and then also organized the peasant schools of Neamț County, serving as inspector.
Proposed innovations he "learned at Paris", now included the establishment of a printing press and the demolition of new additions to the historical site.
However, he was also suspected of giving away boons, including the monastery's cloth factory and a large press, to his patron Kogălniceanu and to the government itself.

Such activism, and also his harsh temper, led to numerous complaints.
The new minister, Dimitrie Rosăt, protected Vârnav.
He scolded those monks who wanted him tried by church tribunal, calling them the "hirelings of Russia".
Vârnav himself had a long-standing feud with Hieromonk Andronic Popovici, whom he accused of using sermons to promote anti-Cuza sentiments and Russophilia.
In September 1861, he obtained Popovici's demotion, prompting the latter to cross over into the Bessarabia Governorate and set up Noul Neamț Monastery outside Kitskany.
Andronic claimed that this establishment was merely a lavra for the old one.
Vârnav, who kept the monastery seal on him, did not validate this in writing, but his adversaries either forged or obtained permission from other administrators.

Eventually, by 1862, Alexandru A. Cantacuzino took over at the ministry and had Vârnav arrested.
Vârnav pleaded for his case and petitioned the Divan with letters also taken up in Tribuna Română gazette.
Archimandrite Timotei Ionescu dismissed his defense as fantasy, depicting Vârnav as a persecutor of his monks, who had loosely interpreted Cuza's policies in order to suppress dissent at the monastery.
According to church historian Melchisedec Ștefănescu, Vârnav, being "detested by the public and disgraced by prince Cuza", settled in Bucharest, "providing his services to whoever would need them."
He sees the former Starets as an extremist and a heretic, "formed in the school of Blanqui, Pyat [and] Rochefort".

Vârnav returned to favor in January 1864, when Dimitrie Bolintineanu, who chaired the unified ministry of education, appointed him to a commission that was tasked with assessing calendar reform.
However, his name was immediately flagged and stricken out by the Metropolitan Bishop, Nifon Rusailă.
Vârnav, who was reportedly a delegate to the Elective Assembly in 1864, supported Cuza's anti-parliamentary coup.
During the incident, he lived in a rented townhouse at Sfântul Dumitru–Poștă Church in Lipscani, shared with Cuza's uncle Grigore.
During the plebiscite of June 1864, organized by the Domnitor, he put up a "lit sign" reading: Popa Vârnav zice da ("Father Vârnav Says [to Vote] Yes").
Also a Cuza loyalist, Constantin Vârnav continued to serve on the Princely Court of Justice, where he notably enforced censorship laws against Ionescu de la Brad.
Returning to live among the monks of Neamț, Vârnav involved himself in the controversy over the secularization of monastery estates. Moldavia's Education Minister, Alexandru Teriachiu, assigned him to a reform committee which uncovered great irregularities at Neamț, including a dysfunctional seminary and an inhumane ward for the insane. Vârnav refurbished the seminary, and then also organized the peasant schools of Neamț County, serving as inspector. Proposed innovations he "learned at Paris", now included the establishment of a printing press and the demolition of new additions to the historical site. However, he was also suspected of giving away boons, including the monastery's cloth factory and a large press, to his patron Kogălniceanu and to the government itself.
Such activism, and also his harsh temper, led to numerous complaints. The new minister, Dimitrie Rosăt, protected Vârnav. He scolded those monks who wanted him tried by church tribunal, calling them the "hirelings of Russia". Vârnav himself had a long-standing feud with Hieromonk Andronic Popovici, whom he accused of using sermons to promote anti-Cuza sentiments and Russophilia. In September 1861, he obtained Popovici's demotion, prompting the latter to cross over into the Bessarabia Governorate and set up Noul Neamț Monastery outside Kitskany. Andronic claimed that this establishment was merely a lavra for the old one. Vârnav, who kept the monastery seal on him, did not validate this in writing, but his adversaries either forged or obtained permission from other administrators.
Eventually, by 1862, Alexandru A. Cantacuzino took over at the ministry and had Vârnav arrested. Vârnav pleaded for his case and petitioned the Divan with letters also taken up in Tribuna Română gazette. Archimandrite Timotei Ionescu dismissed his defense as fantasy, depicting Vârnav as a persecutor of his monks, who had loosely interpreted Cuza's policies in order to suppress dissent at the monastery. According to church historian Melchisedec Ștefănescu, Vârnav, being "detested by the public and disgraced by prince Cuza", settled in Bucharest, "providing his services to whoever would need them." He sees the former Starets as an extremist and a heretic, "formed in the school of Blanqui, Pyat [and] Rochefort".
Vârnav returned to favor in January 1864, when Dimitrie Bolintineanu, who chaired the unified ministry of education, appointed him to a commission that was tasked with assessing calendar reform. However, his name was immediately flagged and stricken out by the Metropolitan Bishop, Nifon Rusailă. Vârnav, who was reportedly a delegate to the Elective Assembly in 1864, supported Cuza's anti-parliamentary coup. During the incident, he lived in a rented townhouse at Sfântul Dumitru–Poștă Church in Lipscani, shared with Cuza's uncle Grigore. During the plebiscite of June 1864, organized by the Domnitor, he put up a "lit sign" reading: Popa Vârnav zice da ("Father Vârnav Says [to Vote] Yes"). Also a Cuza loyalist, Constantin Vârnav continued to serve on the Princely Court of Justice, where he notably enforced censorship laws against Ionescu de la Brad.
Scarlat Vârnav