The visitors were the first team to create an opportunity when Andres Iniesta collected a pass from Cesc Fabregas and thumped an effort towards the top corner, but goalkeeper Esteban got across to make a fine save to deny the Spaniard.
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Barcelona built on a promising opening by taking the lead in the 21st minute when Messi combined well with Pedro on the edge of the box before curling a wonderful effort into the top corner.
Almeria looked like they had the chance to equalise against the run of play as Liverpool loanee Suso collected possession on the edge of the box before getting past Gerard Pique, who brought him down.
The free kick was then whipped into the box by Suso himself, but Barcelona defender Marc Bartra did just enough to get the ball away for a corner.
Barcelona started the second half strongly and added their second of the game in the 57th minute when Fabregas crossed for Adriano, who was left with a simple finish.
Barca nearly added a third a few moments later when Iniesta found Adriano inside the box, but Esteban managed to close down the angle at the vital moment to stop the pass.
The away side continued to push for a third and they nearly grabbed it in the 83rd minute when Bartra found himself with space, but the defender could only poke the ball wide of goal.
Almeria thought that they had pulled one back late on when Sebastian Dubarbier tapped home from close range, but the offside flag had been raised against Ramon Azeez, leaving the final score at 2-0, as Barca continued their unbeaten start to the season.