• Dual accreditation status through the Southern Association of Colleges and Schools (SACS) and The Southern Association of Independent Schools (SAIS)
• South Carolina Independent School Association (SCISA)

Beaufort Academy maintains membership in the following organizations:

• The National Association of Independent Schools (NAIS)
• The South Carolina Independent School Association (SCISA)
• The Palmetto Association of Independent Schools (PAIS)
• The Southern Association of Independent Schools (SAIS)
• The College Board (School Code 410118)
• The National Association of College Admission Counseling (NACAC)
• The National Association of Secondary School Principals (NASSP)
• The Mid-South Independent School Business Officers Association (MISBO)
• South Carolina Association of Non-Profit Organizations (SCANPO)