In the microflow create an activity that retrieves the account from the database where the xpath looks something like:
[EmailID = $Registration/EmailID]
Then after this activity perfrom a aggregate action on the list and get the count, this will optimize the query to perform only the count of the records found.
Then in the decision write the statement like:
$count = 0
When this is true the emailid was not found, else the account using the emailid was found.