Chris McEleny, Alba's general secretary and a former SNP councillor, has been suspended after being accused of gross misconduct.
The suspension comes as party members vie to appoint a new leader following the sudden passing of founder Alex Salmond.
And McEleny, the BBC understands, has also launched a separate complaint against the party's acting leader, former justice secretary Kenny MacAskill.
However, while Alba said it was unable to comment on internal employment matters, it did say there had not been any disciplinary probe into MacAskill.
Last month McEleny announced he was stepping down from his role as general secretary, but it has now been confirmed he was in fact suspended over the allegations of gross misconduct.
The Scotsman exclusively reported that his suspension centred around allegations of "disobeying direct orders from leadership and blocking office bearers from carrying out their duties".