Before starting the certification exercise ensure the room is clean, the HVAC has been running for a period of time to purge the ducting, this can be found by running a particle counter in the room in question for a period of time and ensure the baseline values do not change by more than x percent (x could be 5-10% based on external factors such as weather). Once this has been found and the room are deemed to be stable then run the ISO certification.
For more information, read Particle Monitoring Requirements in Pharmaceutical Cleanrooms.