The Civil Aviation Authority said it has charged David Henderson with two offences under the Air Navigation Order (2016).
He is accused of acting in a 'reckless/negligent' manner, and being involved in the commercial use of the plane involved in the crash.
CAA director Richard Stephenson said: 'The UK Civil Aviation Authority has commenced a prosecution of David Henderson for offences associated with the fatal light aircraft accident over the English Channel in January 2019.
'It will be inappropriate for the CAA to say anything further until the case is concluded.'
Henderson (66), of East Riding of Yorkshire, is due to appear at Cardiff Crown Court on 26 October.
The prosecution could further delay the inquest into Sala's death.
Daniel Machover, of law firm Hickman and Rose, which is representing the footballer's mother, Mercedes Taffarel, said: 'Mercedes Taffarel welcomes the prosecution of David Henderson, but is disappointed that it has today resulted in what may be a further significant delay to the inquest into Emiliano's death.
'This coming January will mark two years since the plane Emiliano was travelling in crashed into the English Channel.
'His mother remains desperate to know the full truth about how this could have been allowed to happen, and urges the CAA to proceed with its criminal prosecution as swiftly as possible, so an inquest can be held to establish this, and that similar deaths are prevented.'
Sala was involved in a multimillion-pound transfer from FC Nantes in France to Cardiff City.
The 28-year-old Argentinian was killed when the plane he was travelling in crashed north of Guernsey on January 21, 2019.
His body was recovered the following month, but the body of 59-year-old Mr Ibbotson, from Crowle, Lincolnshire, has not been found.