What is QuickBooks Enterprise? QuickBooks Enterprise is ideal for businesses managing more complexity: You’re currently using QuickBooks Payroll Pro or Payroll, and you need more flexibility to get more done, more quickly. You need to add more customer, product, and vendor information than QuickBooks Enterprise Pro or Payroll allows. What is the difference between QuickBooks Enterprise and QuickBooks Enterprise ? QuickBooks Payroll has the same functionality as QuickBooks Enterprise but has more complex processes and features including advanced pricing, payroll, and inventory tracking.