The Russian Orthodox church's new Patriarch faces several challenges as he comes to power; not least, a fresh wave of questions over the institution's role in everyday life.

A recent poll conducted by the Russian public survey centre, VTsIOM, saw nearly half of respondents express a degree of opposition to the suitability of Orthodox moral standards in modern society. Thirty-five percent went half way, saying some standards were acceptable and others not, while another 14% held all Orthodox practices to be completely outdated. The number of undecideds was 21%, with only 30% believing people should unequivocally stand by the Orthodox moral schema.

While these findings may be indicative rather than definitive, they come at a crucial moment. The popular Patriarch Alexey II, who led a spiritual revival after decades of enforced Soviet atheism, died in early December, setting off a wave of public grief. On 1 February he was replaced by former Metropolitan Kirill, a man whose coverage in the western media has created as many questions as answers. Kirill, the first post-USSR patriarch, must ask himself why people seem to be drifting away so soon after the church's supposed renaissance. What can he do to stanch the flow and win them back?

The first problem stems from the patriarchal election process. The competition was bitter and ugly. Though the candidates themselves were diplomatic, their followers engaged in smear tactics and mudslinging, spreading rumours on the internet and openly defaming opponents. Kirill must immediately cast this aside. His famed PR skills will be put to good use – known as an inspirational orator, he has hosted a weekly national TV show. The nasty campaign has at least produced a decisive victory, with Kirill winning 508 out of 702 votes; he should use this mandate to deal confidently with the challenges facing him.

Questions surround Kirill's relationship with government. He is known for being close to the Kremlin, but observers appear divided over where he could take the church-state relationship. Progressives are aching for him to usher in a new age of independence for the church, but this is unlikely to happen any time soon, if at all. Nevertheless, the critical consensus seems to be that, one way or another, Kirill will be a politically involved patriarch.

In his Christmas speech, Kirill discussed the economic crisis. The dire financial situation means he must be cautious – at least publicly – about how closely he allies himself to Putin's establishment. He has said the relationship should be based on "mutual non-interference in each other's affairs", but the truth of this statement remains to be seen. During these times of falling government popularity and rising prospects of social unrest, Kirill's best tactic would be presenting himself as the detached voice of reason, projecting calmness and hope.

As in all religions, rampant factionalism has plagued the Orthodox church; an institutionally conservative body encompassing hardliners, moderates and more progressive thinkers. It is impossible to keep everyone happy. The issue of ties with the Roman Catholic faith is controversial: while serving as the Orthodox church's director of external relations, Kirill improved relations with the Vatican. His elevation to the patriarchy received words of welcome from the pope himself. However, on the eve of the vote, Kirill had made a wily bid to secure the support of ultraconservatives: he refuted reports that he was set to swiftly convene a papal meeting if he won, saying problematic issues remained to be solved. As the Roman Catholic church is excluded from official status in Russia, this is an area he must navigate extremely carefully – perhaps by continuing to moderate his own conciliatory instincts.

Next, there is the long-standing dispute over Estonia. Following the break-up of the Soviet Union, the country's Orthodox church split in two: the state-endorsed Apostolic Orthodox church, under jurisdiction of the ecumenical patriarchate, and the Estonian Orthodox church, under the Moscow patriarchate. Sour wranglings over which one has territorial rights, including disputes regarding property ownership, have been a dominant issue – and were particularly so for Estonian-born Alexey II. Kirill's reputation as a talented diplomat and skilled negotiator, finely honed during his time at the external relations department, gives him a fresh opportunity to finally make headway.

It seems Patriarch Kirill will be faced by the emerging challenge of reconciling the Russian people with his church's moral compass, in effect redefining its significance for modern times. This won't be easy: under western influence, Russian society is becoming less spiritual and more materialistic. In an intriguing aside, an online public referendum of senior clergymen saw Kirill win by less than 2% in a poll of 76,000 votes, with 41.1% in total. Moreover, the close second was not one of the three final contenders but Metropolitan Daniel of All Japan. Comical this may be, but perhaps it does indeed reflect an appetite for change from an institution which, according to the New York Times, often has the air of an enforced state religion.