David Villa got the goalscoring underway by netting with a quarter of an hour gone, before Diego Costa's penalty doubled the hosts' advantage.
Rodri halved the deficit before half-time, but Atleti were far superior in the second period, with Tiago Mendes and Raul Garcia getting in on the act, before Alex Vidal got a late consolation goal.
Atletico boss Diego Simeone made three changes from the team that beat Real Sociedad in their last game. Garcia came in for Arda Turan, Tiago for Mario Suarez, while Uruguayan centre-back Jose Maria Gimenez made his debut, standing in for Joao Miranda, who was absent with a fever.
Garcia tried his luck early on with an audacious over-head kick, which went just over the bar. Shortly afterwards, the opening goal arrived.
Almeria defender Angel Trujillo headed a cross into the air, but Villa was waiting for it, and patiently let it drop before volleying into the bottom corner.
Diego Costa came close to what would have been a spectacular solo goal, snaking his way through the Almeria defence, but was unable to beat goalkeeper Esteban Suarez as he approached the goal.
Costa eventually got on the scoresheet, sending Esteban the wrong way from the penalty spot, after Filipe Luis was tripped in the area by Hernan Pellerano.
Almeria managed to get a goal back just before half-time, Rodri firing high into the net after recovering the ball inside the area.
The visitors had given a decent enough account of themselves in the first half but wilted in the second, as Atleti turned up the heat.
Koke Resurreccion rattled the cross bar just a minute after the re-start from outside the area, then Gabi Fernandez forced a fine stop by Esteban, who got down low to divert a shot headed for the bottom corner, following a cutback from Costa.
Raul Garcia also came close to getting the third, shooting just wide of the far post.
The hosts finally got their third following a perfectly executed move from a free-kick. Gabi quickly played a low pass to Tiago by the penalty spot, catching the Almeria defence unaware, and the Portuguese poked the ball into the bottom corner.
Only four minutes later, the game was put beyond Almeria's reach.
Juanfran cut the ball back from the right hand side to Raul Garcia, who backheeled it into the net.
There was still time for one final goal, however, Alex Vidal beating Courtois from inside the area, as the Atleti defence relaxed.
While Atletico maintained their 100 per cent start to the season, Almeria are struggling in their first year back in the top flight, and are still without a win.