Following the Georgian Civil War, his party formed an alliance with the authoritarian leader of Adjara Aslan Abashidze and he was elected to a second term as MP in 1999, during which he became an opponent to President Eduard Shevardnadze.

A vocal critique of President Mikheil Saakashvili, Sanikidze joined the Georgian Dream coalition as it defeated UNM in 2012 and won a fourth term in Parliament as Majoritarian MP from Kutaisi.

He successively served as Chairman of the Diaspora and Caucasus Committee, pushing for closer ties between Georgia and Iran, and as Vice Speaker of Parliament.

In 1990, he joined the Union of Georgian Traditionalists (UGT), one of the first legally-recognized political parties in Soviet Georgia, a conservative organization supporting independence and monarchism.

In opposition to President Eduard Shevardnadze, he served as deputy chairman of the UGT faction in Parliament, maintaining the post after the party split away from Revival.

[2] During the 2003 parliamentary elections, his party joined Speaker Nino Burjanadze's forces to form the National Democratic Alliance and Sanikidze was 18th on the coalition's electoral list.

[3] Despite winning a seat in that year's race, the Rose Revolution led to the cancellation of the results and his party failed to gather enough votes in the subsequent 2004 elections.

"[13] He rapidly became one of the most radical opponents to Saakashvili, calling for his resignation,[14] blaming him for the Russia-Georgia War and comparing him to Chechen leader Aslan Maskhadov,[15] originally refusing any talks with the government to put an end to the political crisis,[16] and organizing a blockade of the East-West Highway in May 2009 during NATO-Georgia military exercises.

As an MP elected from the ruling party coalition, Gubaz Sanikidze became one of the highest-ranking members of Parliament, selected as Chairman of the Diaspora and Caucasus Affairs Committee as a personal choice of Prime Minister Bidzina Ivanishvili.

The first fissure within the GD coalition that saw the departure of the Free Democrats from the party and the resignation of Vice-Speaker Zurab Abashidze allowed Gubaz Sanikidze to succeed him on the post on 19 February 2015.

[46] Without a seat in Parliament and having left the NF, Gubaz Sanikidze became an unaffiliated political commentator, often appearing on media to criticize the government, while rejecting any cooperation with UNM, at the time the largest opposition party.

[47] On 11 June 2019, he became a co-founder of Victorious Georgia, a new political party set up by former controversial Defense Minister Irakli Okruashvili,[48] with the stated goal of continuing reforms that it claimed had been abandoned by Georgian Dream.

[49] Following Okruashvili's arrest a week later as one of the leaders of an anti-Russian protest that tried to enter the Parliament building, Sanikidze called him a political prisoner and stated that "[Bidzina] Ivanishvili has a mental disorder and takes direct orders from Vladimir Putin.

This move was heavily criticized by former National Security Council Secretary Giga Bokeria, who accused UNM of "betraying the values of the Rose Revolution".

[54] A leaked phone call recording between Sanikidze and Temur Alasania, a wealthy businessman with close ties to the international arms trade and uncle of Saakashvili, revealed discussions over the proclamation of an "alternative government"[55] and the forceful overthrow of the sitting authorities.