VBA code to set date format for a specific column as "yyyy-mm-dd"

Use the range's NumberFormat property to force the format of the range like this:

Sheet1.Range("A2", "A50000").NumberFormat = "yyyy-mm-dd"

You are applying the formatting to the workbook that has the code, not the added workbook. You'll want to get in the habit of fully qualifying sheet and range references. The code below does that and works for me in Excel 2010:

Sub test()
Dim wb As Excel.Workbook
Set wb = Workbooks.Add
With wb.Sheets(1)
    .Range("A1") = "Acctdate"
    .Range("B1") = "Ledger"
    .Range("C1") = "CY"
    .Range("D1") = "BusinessUnit"
    .Range("E1") = "OperatingUnit"
    .Range("F1") = "LOB"
    .Range("G1") = "Account"
    .Range("H1") = "TreatyCode"
    .Range("I1") = "Amount"
    .Range("J1") = "TransactionCurrency"
    .Range("K1") = "USDEquivalentAmount"
    .Range("L1") = "KeyCol"
    .Range("A2", "A50000").Value = Me.TextBox3.Value
    .Range("A2", "A50000").NumberFormat = "yyyy-mm-dd"
End With
End Sub

It works, when you use both lines:

Application.ActiveWorkbook.Worksheets("data").Range("C1", "C20000") = Format(Date, "yyyy-mm-dd")
Application.ActiveWorkbook.Worksheets("data").Range("C1", "C20000").NumberFormat = "yyyy-mm-dd"