The EU27 will choose a winner for each agency after up to three rounds of secret voting.
The application procedure to host the two UK-based EU agencies formally came to a close this week.
The European Commission will now assess all offers on the basis of the criteria set out by its President Jean-Claude Juncker and Donald Tusk, his Council counterpart.
A Commission source said, "In order to allow for a smooth and timely relocation of the two agencies, a final decision will be taken at the general affairs council in November."
Interested member states had until midnight on 31 July to submit their offers to the European Commission and the Council.
The cities bidding to host the EMA as of 1 August 2017 are: Amsterdam; Athens; Barcelona; Bonn Bratislava; Brussels; Bucharest; Copenhagen; Dublin; Helsinki; Lille; Milan; Porto; Sofia; Stockholm; Malta; Vienna; Warsaw and Zagreb.
The European Medicines Agency (EMA) is responsible for the scientific evaluation, supervision and safety monitoring of medicines in the EU.
These are the cities seeking to host the European Banking Authority (EBA): Brussels; Dublin; Frankfurt; Paris; Prague; Luxembourg City; Vienna and Warsaw.
The EBA works to ensure effective and consistent prudential regulation and supervision across the European banking sector.
The applications will be assessed on the basis of six criteria accessibility of the location; schools for the children of the staff and access to the labour market and healthcare for the employees' families.
The decision to relocate the EMA and the EBA - both of which are currently situated in London - is for the governments of member states to take. Their relocation is a direct consequence of the UK's decision to leave the European Union. It does not form part of the Brexit negotiations.
The Commission has repeatedly called for a quick decision on the transfer, as the EMA and the EBA are seen as being two key EU regulatory bodies which must continue to function smoothly and without disruption beyond March 2019.