Vibration protection in a compressor system with a variable speed compressor may include operating a variable speed compressor of a compressor system at a first frequency, measuring a vibration of the compressor system at the first frequency, determining whether the vibration exceeds a maximum vibration value, and operating the variable speed compressor at an average frequency equivalent to the first frequency, when the vibration exceeds the maximum vibration value, by identifying an allowed upper frequency and an allowed lower frequency, calculating an upper operating time and a lower operating time, and operating the variable speed compressor at the allowed upper frequency for the upper operating time and the allowed lower frequency for the lower operating time.