In Rome, hundreds gathered at Piazza dei Cinquecento outside Termini Station.
Students and grassroots union members blocked traffic while chanting, “Let’s block everything for the Flotilla and for Palestine.”
Police shut several metro stations and restricted access to the terminal.
Demonstrators later planned to march toward Piazza Barberini, with nearly a thousand expected to join.
Two major Italian unions, USB and CGIL, announced a nationwide strike for Oct. 3 in protest.
In Barcelona, protesters rallied outside Israel’s consulate, condemning the raid and voicing solidarity with Gaza.
Berlin saw demonstrators gather at Central Station, while in Brussels, crowds marched from Place de la Bourse to the Belgian foreign ministry.
Hundreds more are set to mobilize in London on Thursday.
Organizers of the Global Sumud Flotilla said Israeli warships jammed communications before storming the vessels.
The International Committee for Breaking the Siege on Gaza confirmed that Israeli forces seized the ships Alma and Sirius.
Activists posted videos showing naval boats ordering the convoy to divert course.
The flotilla carried humanitarian and medical supplies, departing in late August and scheduled to arrive in Gaza on Thursday morning.
It was the first time in years that nearly 50 ships—transporting 532 civilian supporters from more than 45 countries—sailed together toward the besieged enclave of 2.4 million Palestinians.
Gaza has endured an Israeli blockade for about 18 years, as well as a genocidal war for about three years.