Peter Boddy, who owned the business in Todmorden, West Yorkshire, and David Moss, who was manager, are accused of breaching food regulations that say meat should be traceable from field to fork.
Criminal proceeding were instigated following a joint investigation by the Food Standards Agency, Dyfed Powys Police and Calderdale Council.
It is claimed that they each committed two breaches of Regulation 4 of the General Food Regulations 2004 between July 2012 and February 12, 2013.
Moss is also charged with one count of forgery over claims that he faked an invoice for the sale of horse meat.
The pair are due to appear at Westminster Magistrates' Court on April 14.
It is not being alleged that the horse meat was being sold as another meat.