[6][7] At the 11th ASEAN Football Federation Council meeting in Naypyidaw on 21 December 2013, Myanmar and the Philippines were named as co-hosts the group stage of the tournament.

[8] The Philippine Football Federation (PFF) initially withdrew as co-host of the group stages in February 2016, citing issues with the Rizal Memorial Stadium as well as the availability of another venue.

[12] On 7 March, the AFF accepted the appeal of the Philippines while Malaysia were named 'standby host', with Vietnam and Singapore withdrawing their bids.

[14] On 12 March, it was confirmed that the Philippines retained hosting rights, following an AFF Council Meeting in Da Nang, Vietnam.

The PFF was able to present a contract with the PSS to the AFF as well as a letter of guarantee from the Philippine Sports Commission.

The draw for the 2016 AFF Championships was made on 2 August 2016,[21] with Indonesia placed in the bottom pot after the FIFA's suspension.

On 23 November, three days before the match between Malaysia and Myanmar, the Malaysian Minister of Youth and Sport Khairy Jamaluddin said that he had petitioned his country football association to boycott Myanmar as the group B host because of Myanmar government's alleged persecution to the Rohingya Muslims after repeated calls from West Malaysian Malay Muslim individuals and political groups of United Malays National Organisation (UMNO), Pan-Malaysian Islamic Party (PAS), People's Justice Party (PKR), National Trust Party (AMANAH) Penang branch as well from Malay extreme group of Pertubuhan Pribumi Perkasa to boycott the country.

[31] In response, the ASEAN Football Federation (AFF) warned Malaysia if they suddenly withdraw from the ongoing tournament without giving any valid reasons for the team problems just because of political concerns, the Football Association of Malaysia (FAM) will facing a long-term sanction from FIFA for letting political interference spread into the association.

[36] During the second leg of the semi-final match in Hanoi between Indonesia and Vietnam, the decision by China referee Fu Ming was deemed as bias by most Vietnamese supporters as the referee did not give any action for any fouls committed by the Indonesian side, while heavily punishing the Vietnamese side when their goalkeeper Trần Nguyên Mạnh given a red card on the 76th minute in a sudden controversial decision.

[41][42][45] At the first leg final in Bogor between Indonesia and Thailand, while Thai player Theerathon Bunmathan was taking up a free kick, his face was seen targeted with green laser light from Indonesian supporters.

During the media session shortly after the end of the match, Thai coach Kiatisuk Senamuang openly stated about the laser light attacks affecting their team performances, in which it was also acknowledged by Indonesian coach Alfred Riedl who "criticised and felt shame on the behaviour of some of the Indonesian supporters although they won the first leg match in their home ground as their victory in the match could be perceived as unfair by their team opponent because of the incident".

[54] His action were however not condemned by most Indonesian supporters and instead been back up by them, with the blame was put to the Thai side for their lacking of sportmanship in the event.