Medical Assistant Salary in Colorado. According to the Bureau of Labor Statistics, the average medical assistant salary in Colorado is 32,790 dollars. The higher end of the pay scale pays approximately 43,000 dollars while the lower end pays around 25,000 dollars. Positions in Colorado have an average higher than the national average of 30,780 dollars. Most medical assistant positions can be found in physicians’ offices; however, the pay is on the lower end of the spectrum.