Three protesters dived into the water to try to stop a ferry carrying 45 Pakistani men as it left Lesbos but were fished out by coastguards.
Other protesters tried to enter the gates of the port, Mytilene.
Some 200 mainly Pakistanis were deported on Monday but the process stalled as asylum applications surged.
Under the EU deal with Turkey, migrants who have arrived illegally in Greece since 20 March are expected to be sent back to Turkey if they do not apply for asylum or if their claim is rejected.
And for each Syrian migrant returned to Turkey, the EU is due to take in another Syrian who has made a legitimate request.
Each person being deported is accompanied by a guard from the EU’s border agency, Frontex.
A Frontex spokesperson said there had been no trouble bringing the migrants from a camp to the port.
“There were escorts with each returnee plus a back-up team,” Ewa Moncure told reporters. “Also, in addition, on board the ferry there was a doctor and translators.
“Now on the way to Turkey, migrants will be given water and breakfast. They all had return decisions. Nobody indicated to our escorts last-minute that they would like to apply for international protection.”
Greek customs officials told the BBC that 140 people would be travelling on two boats on Friday, with the second carrying 95 from other islands.
Of those being returned to Turkey on Friday, the non-Syrians will be taken to deportation centres while any Syrians will be taken to refugee camps to take the place of Syrian refugees who will be directly resettled in the EU.
But Turkey’s President Recep Tayyip Erdogan said on Thursday that his country would only implement the deal if the EU stuck to its side of the bargain:
A further €3bn (£2.4bn; $3.4bn)
Galvanising Turkey’s EU accession process
Granting Turks visa-free travel to the EU’s Schengen area by the end of June
“If the European Union does not take the necessary steps, then Turkey will not implement the agreement,” Mr Erdogan said in a speech at his presidential palace in Ankara.
But German Chancellor Angela Merkel, whose country has taken in the bulk of the asylum seekers so far, said on a visit to France she was “very happy”.
The small group of protesters in Mytilene chanted “EU – shame on you”.
The returns arrangement has alarmed rights groups, who say Turkey is not a safe country for migrants.
People detained on Lesbos and Chios have virtually no access to legal aid, limited access to services and support, according to Amnesty International.
Migrants on the Greek border with Macedonia clashed with police on Thursday, demanding that the border be reopened so they could continue with their journey that way.
One million migrants and refugees have entered the EU by boat from Turkey to Greece since early last year.
Many are keen to travel to Germany and other northern EU countries and experts have warned the deal could force them to take alternative, more dangerous routes.