The Gunners have made a stuttering start to the season with a defeat to Liverpool and a pulsating draw with Tottenham to leave them seventh in the Premier League table.
Ex-Gunner Alan Smith has claimed that the players have struggled to assimilate the system he is trying to implement, but Fowler believes time is the key.
There have been whispers of the players not getting him or understanding his tactics, but I think youve seen enough already from him to believe he can get it right there, Fowler told the Mirror.
There are problems, obviously. Even I was baffled by his tactics at Anfield. They could have lost 7-1 there, because they were taken apart in a spell after half-time.
Yet they got to the Europa League final in his first season, and hes putting together a decent side, with an incredible attack.
Arsenal smashed their club record signing to bring in Nicolas Pepe over the summer to join an attacking corps that already boasts the likes of Pierre-Emerick Aubameyang, Alexandre Lacazette and the enigmatic Mesut Ozil.
The Gunners defence has been strengthened too by David Luiz and Kieran Tierney, although the latter is still recovering from a hip injury, and Fowler knows that teams can take time to gel.
I think hes a coach who likes to create a different plan for each team he faces, and that can be a learning process for some players, Fowler added.
Yet Jurgen Klopp does that too. Watch Liverpool closely, and they tweak their tactics each game, to exploit weakness in the opposition.
Emery is a manager who can cope with egos and get the best from players. I remember when he took Klopps side apart in the second half of the 2016 Europa League final, with a brilliant tweak of his tactics.