The Spanish midfielder missed Saturday's win at Leeds United due to the injury.
And Arsenal have now confirmed surgery is needed, with a statement reading: “Further to sustaining a foot injury towards the end of our game against Manchester United on January 25th, subsequent assessments and specialist reviews have confirmed Mikel Merino has a bone injury in his right foot.
“Mikel will have surgery in the coming days and will then begin his recovery and rehabilitation programme.
“Mikel is expected to be out of action for an extended period, with the aim of returning to full training before the end of the season.
“Everyone is fully focused on supporting Mikel to ensure he is back to full fitness as soon as possible.”
For the moment, there is no timeline set for Merino’s recovery. However, there are concerns that he could be sidelined for the remainder of this season.
Taking to Instagram, Merino wrote: “Time to stop now with a foot injury.
“Sometimes life throws this kind of challenge when it is less convenient. Just another opportunity to be strong, resilient and overcome it. We have the best medical team and together we will come back stronger.
“Thank you all, your support means everything to me and I can’t wait to be back on the pitch soon, helping my team and doing what I love.”