A surgical instrument includes a shaft assembly, an ultrasonic blade, and a cleaning device. The shaft assembly includes a first tube and an acoustic waveguide. The first tube has a first inner diameter and a distal end. The waveguide has a first outer diameter. The waveguide extends within the first tube. The first outer diameter of the acoustic waveguide and the first inner diameter of the first tube together define a gap. The ultrasonic blade extends distally from the distal end of the first tube. The acoustic waveguide is configured to communicate ultrasonic energy to the ultrasonic blade. The cleaning device is configured to actuate within the gap to thereby clean at least a portion of the shaft assembly and/or at least a portion of the ultrasonic blade.