The Liga club narrowly avoided relegation back to the second tier last season, taking 10 points from their final four games to beat the drop by a point.
Francisco has been rewarded with a fresh deal, with Almeria citing his "great work" as the reason for his extension in a statement on their official website.
The 35-year-old coach spent time with Almeria's reserves before taking on the top job and his first task after signing will be stabilising the club's leaky defence.
Only one side in the bottom half of last season's table - Rayo Vallecano - scored more goals than Almeria.
But they shipped 71 goals in 38 matches and are likely to require improvement if they are to retain their top-flight status again.
LATEST ARTICLES