Last week's first leg in Santander, which ended 1-1, was disrupted when a group of disgruntled fans tried to storm the VIP tribune, and Spanish police have launched an investigation after a security guard needed stitches in a head wound.
The home team also staged a brief protest over unpaid wages by standing still for around 10 seconds after kickoff and only began playing when their opponents obligingly put the ball into touch.
Santander have fallen on desperately hard times since they were taken over in January 2011 by Indian businessman Ahsan Ali Syed, who set out his vision of a bright future for the north coast club.
However, they were relegated from La Liga at the end of the 2011-12 season after finishing 10 points adrift at the bottom of the table. Ali Syed disappeared from view and the club's crisis deepened as they dropped down to the third tier at the end of last term.
The future looked bleak after a capital increase in October designed to save them from ruin flopped and had to be abandoned and they remain mired in bankruptcy proceedings.
Current president Angel Lavin, the target of last week's protests, has pledged to do all he can to rebuild a team like the one that qualified for Europe when they finished sixth in La Liga in 2007-08.
"I have the soul of a sailor and I have to be the last person to abandon ship," Lavin said last week as he condemned those behind the attack on club officials.
If they manage to get past Almeria, Santander will play Real Sociedad or Villarreal, who drew their first leg in San Sebastian 0-0 and meet at the Madrigal on Thursday (1900), in the quarter-finals.
On their side of the draw they also have Barcelona, who have a 4-0 cushion when they play at Getafe on Thursday (2100).
Barca have Lionel Messi back after a two-month injury absence although the Argentina forward was unable to break the deadlock when he played the second half of Saturday's 0-0 draw in the top-of-the-table La Liga clash at Atletico Madrid.
Barca's Spain playmaker Andres Iniesta is a doubt after he took a knock to his left knee in the Atletico game and had to be replaced by Messi.
Cup holders Atletico have work to do when they host Valencia on Tuesday (2030) after last week's first leg at the Mestalla ended 1-1.
Atletico have a potential meeting with local rivals Real Madrid, whom they beat 2-1 in last year's final at Real's Bernabeu stadium, in the last four.
Real beat Osasuna 2-0 at home last week and play the return in Pamplona on Wednesday (2030).
Second-division Alcorcon surprised Espanyol 1-0 in their first leg and the pair clash in Barcelona on Wednesday (1830).