EES started to be rolled out in October last year and is now fully up and running.
The time it takes to register biometric information means people have been told to prepare for a wait at border controls.
During the introductory period, queues started to flare up at certain airports at busy times.
Since then, the system has been working well in some airports, while waits of several hours have been reported at others.
A representative of airline trade body IATA has warned queues in some places could be as long as six hours.
Travel experts and industry figures have blamed problems with the technology and border staffing levels. There have also been reports of people having to register their biometric information more than once.
The UK boss of Wizz Air told the BBC passengers should be prepared for a wait, and turn up three hours before their flight home.
Some passengers have missed flights home because the wait for EES checks meant they could not reach their gate in time.
Whether airlines will hold flights for passengers who get held up is a mixed picture. Some say they will wait wherever possible, while Ryanair is an example of a carrier which has said it will not.
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The summer holidays will provide a major test of the new system.
Greece is not applying the biometric checks to British visitors over the peak period.
The European Commission is allowing the system to be suspended in “exceptional circumstances that lead to excessive waiting times”, until September.
Improvements are planned in some places which have seen the worst queues. For example, Portugal has announced hundreds of extra border staff for July.
Airports say passengers should follow the advice of their airline when it comes to how early to arrive for flights back to the UK.
What about ferries and trains?
At a few locations, French border police conduct passport checks before people leave the UK.
They are Dover’s ferry port, Eurotunnel’s Folkestone terminal, and Eurostar’s St Pancras rail terminus.
For months, dozens of automated machines have been in place at these locations for people to go through EES.
They are not yet in routine use. Border staff are doing part of the process instead.
At Dover, despite the fact fingerprints and photos were not yet being collected, long queues of cars built up the start of the May half term holidays. French border authorities ended up suspending the process.
Coaches will be sealed after passengers have completed EES checks, before driving over to the ferry terminal.
A mobile phone app has been developed to enable passengers to do part of the process before reaching the border.
However, the app is currently being used by only two countries. Sweden is using it to help with the registration of passport data and photos. Portugal is only using it for an entry questionnaire.
What is ETIAS and when is that coming?
The EU is also introducing a new visa waiver system linked to passports called the European Travel Information and Authorisation System (ETIAS), which will build on the EES.
Citizens of non-EU countries who do not need a visa to enter the EU – including people from the UK – will be able to apply online for authorisation before they travel.
ETIAS is not due to start until the end of 2026, but the final date has not yet been confirmed.
It will cost €20 (£17.47) per application, and will be valid for three years.
People aged under 18 and over 70 will need to apply, but will not have to pay.
Additional reporting from Kris Bramwell.
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