On 18 July 2016, an independent investigation commissioned by World Anti-Doping Agency concluded that it was shown "beyond a reasonable doubt" that the RUSADA, the Ministry of Sport, the Federal Security Service (FSB) and the Centre of Sports Preparation of the National Teams of Russia had "operated for the protection of doped Russian athletes" within a "state-directed failsafe system" using "the disappearing positive [test] methodology."

It was used on 643 positive samples, a number that the authors consider "only a minimum" due to limited access to Russian records.

[2] IPC president Philip Craven stated that Russia's actions had demonstrated a failure in its obligations to comply with established anti-doping protocols.

[10] On 18 July 2016, the World Anti-Doping Agency (WADA) published a 97-page report by Canadian attorney Richard McLaren, covering significant state-sponsored doping in Russia.

It found that Russia's Ministry of Sport and Federal Security Service (FSB) had operated a "state-dictated" system to implement an extensive doping program, which included the use of a "disappearing positive methodology" (DPM) – the process of swapping out positive urine samples for clean ones in order to evade detection.

[21] The next day, following a request for an appeal by the RPC, the Federal Supreme Court of Switzerland also upheld the CAS's decision.

[22] During the entry of Belarus at the opening ceremony's parade of nations, Andrey Fomochkin—a member of the country's Ministry of Sport, was seen holding a Russian flag as a display of solidarity to its neighbour.

The flag was quickly confiscated by officials; after he was identified, Fomochkin's accreditation was revoked by the IPC for violating policies which forbid political protests and gestures.

The IPC also warned that it would closely monitor medal presentations involving Belarusian athletes to ensure they do not display political gestures.

[23][24] Fomochkin's actions were praised by Belarusians (including President Alexander Lukashenko), as well as Maria Zakharova—a member of Russia's Ministry of Foreign Affairs; she stated to a news agency that Fomochkin had "[shown] solidarity with people who were disgracefully treated in an inhumane way in not being allowed to compete at the Paralympics".

Playing in Group B, Russia opened the tournament with a 1–0 victory against France, followed by two 0–0 draws against Belgium and Spain.

[26][27] The Russia national 7-a-side football team qualified for Rio 2016 after winning the 2015 CP World Championships, defeating reigning European champions Ukraine.

Among the archers that had qualified included Bato Tsydendorzhiev, Margarita Sidorenko, Svetlana Barantseva, Irina Rossiyskaya, Sergey Khutakov, Anton Zaypaev and Stepanida Artakhinova.

[36] Being among the highest-ranked countries on the men's and women's UCI Para-Cycling Nations Ranking Lists as of 31 December 2014, Russia qualified for Rio 2016, assuming they continued to meet all other eligibility requirements.

[43][44] Russia earned a qualifying spot in the inaugural Paracanoeing competition following their performance at the 2015 ICF Canoe Sprint & Paracanoe World Championships in Milan, Italy, where the top six finishers in each Paralympic event earned a qualifying spot for their nation.

Sergey Nochevnoy gave Russia their fourth spot at Rio, this time in the R3 – 10Mm Air Rifle Prone Mixed SH1 event.

[49][50][51] Three opportunities to qualify were available through the 2015 IPC Shooting World Cup events in Osijek, Sydney, and Fort Benning.

[50][55] The top two finishers in each Rio medal event at the 2015 IPC Swimming World Championships earned a qualifying spot for their country.

Iurii Luchkin earned Russia's ninth spot in the Men's 100m Breaststroke SB5 with a gold medal finish.