If you need to process payroll for more than 1 employer identification number, QuickBooks Enhanced Payroll is the clear winner. At 52 pay periods per year, our chart shows QuickBooks Enhanced Payroll costs $911.80. For 2 or 3 companies, that cost doesn’t change. For QuickBooks Online Payroll Plus, it jumps to $1260 for 2 companies and $1890 for 3. That’s a jump of 38% and 107% respectively.