Florida Medical Office Manager Salary Information. The average yearly salary for Medical Office Manager in Florida is $41,523.If you are just beginning to work a new job as a Medical Office Manager in Florida, you could earn a starting pay rate of $34,195 annually.As is true for most jobs and careers, you can expect your hourly pay rate or salary to increase as you gain experience and the longer you are employed with the same employer.f you are just beginning to work a new job as a Medical Office Manager in Florida, you could earn a starting pay rate of $34,195 annually. As is true for most jobs and careers, you can expect your hourly pay rate or salary to increase as you gain experience and the longer you are employed with the same employer.