He will take over from William Walker, who announced that he will retire earlier this year.
Watkins has worked in the timber and furniture industries for the past 25 years. Previously, he was health, safety and environmental consultant at The Furniture Industry Research Association.
PEFC UK chairman Peter Latham said: "We are confident that Alun's previous experience in the timber and furniture industry and knowledge of certification will be invaluable in helping PEFC to strengthen its position in the UK market."
Walker took on the job of national secretary at PEFC in 2005 and has since helped boost the number of companies with PEFC certification from 70 to 1,300.
Latham said: "The board recognises the immense contribution William has made to the organisation and we now look forward to his successor building on the firm foundations laid down."