A noise mitigation boot that can be installed on or integrated into a miniature diaphragm pump to reduce the overall noise and improve sound quality during operation. The diaphragm pump includes a housing having first and second ports and an interior chamber, a pumping diaphragm disposed in the interior chamber and dividing the interior chamber into a pumping chamber and a backside chamber, a motor for reciprocating the pumping diaphragm for pumping air into and out of the pumping chamber, and flow passages connecting the pumping chamber to the first and second ports. The first port is configured for attachment to a flow line and the second port opens to an exterior surface of the housing. The noise mitigation boot has a muffler wall overlying the exterior surface of the housing. The muffler wall has formed therein a passage extending from the second port to the backside chamber for effecting fluid communication between the second port and the backside chamber.