Border Force members of the Public and Commercial Services union (PCS) are in dispute with the Home Office and are striking over pay, pensions, jobs and redundancy.
The first walkout over 23-26 December passed off without significant disruption, though, with Heathrow claiming travellers experienced "no issues", and there being few additional reports of major delays or hiccups.
Walkouts were also staged at Birmingham, Cardiff, Gatwick, Glasgow and Manchester airports, and had threatened to disrupt up to 10,000 flights between 23 December and 31 December.
The PCS union has warned the action could continue until May following a successful strike ballot in November.
Civil servants and military personnel have stood in to staff passport control at the six affected airports, as well as at the ferry port of Newhaven.
A Home Office spokesperson told passengers to be prepared for disruption, but stressed it was working closely with airports and port operations to minimise disruption and ensure there were adequate provisions for passengers in the event of longer queues.
Sky News reported passengers travelling to London from Brussels on Eurostar faced significant delays when their passports were required to be checked again following an incident at Lille, where just two UK Border Force stations were staffed.