Has anyone measured DE0-Nano EMI emissions?

I am working on a system where a DE0-Nano board is used to record microphone data from PDM microphones. But I've noticed that the EMI associated with the FPGA board is causing a lot of noise in the data received from the microphones. The FPGA board is plugged into a custom "motherboard" PCB that connects the FPGA to a BeagleBone Black (BBB) via SPI. I've been able to remove the noise associated with EMI by enclosing the motherboard PCB with the FPGA and BBB in a cardboard box wrapped in aluminum foil. I've also noticed that it is equally effective to enclose only the FPGA and keep the BBB outside of the box. From this I've concluded that the BBB is not contributing in any significant way to the EMI affecting the microphones. Now I'm trying to determine if the EMI is coming from somewhere on the DE0-Nano FPGA board or if it could have something to do with the custom motherboard PCB. Does anyone have any measurements on EMI produced by the DE0-Nano FPGA by itself? or know of any way to reduce the EMI produced by the FPGA?