Xero calculates tax on a per-line basis, rounding to two decimal places, and then sums the tax totals of each line to calculate the total invoice tax. Other systems may total lines and then calculate the tax amount, which can lead to a slight variance.

Let's use the example below of a bill from a New Zealand company to a New Zealand company, where GST/VAT is applied at 15%.
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Invoice line 1: Product A @ $25.06, tax at 15%: $3.76 line total: $28.82
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Invoice line 2: Product B @ $25.61, tax at 15%: $3.84 line total: $29.45
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Invoice line 3: Product C @ $25.63, tax at 15%: $3.84 line total: $29.47
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Xero totals: Subtotal: $76.30, Tax: $11.44
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Xero document total: $87.74

Another system total: Subtotal: $76.30 + Tax @ 15%: 11.45
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This can be illustrated below in Xero, as the approach is the equivalent of just having one line in Xero:

To compensate for this, Lightyear will send into Xero an extra rounding row, in this occasion of -$0.01 (not taxed). To this GL Code we will assign the default Rounding GL that's set up in your Xero account. Whilst this action will not fix the GST/VAT amount, it will balance the total of the bill, meaning you will be paying the supplier the correct amount of money.

Set the bill view in Lightyear to Tax Exclusive. This adjustment ensures that tax calculations in Lightyear align more closely with Xero’s expectations, reducing potential rounding discrepancies.

In Xero, head to your Chart of Accounts and search for the Rounding GL Code. Ensure this is set up as Code: 860 and Description: Rounding. If it isn't, your export may fail.

​Back in Lightyear, go to Accountancy > GL Codes and make sure this same GL Code matches what's set up in Xero, and ensure the code is Active. If discrepancies persist, consider re-exporting the bill from Lightyear or manually editing the bill in Xero to include the rounding adjustment, ensuring the total matches the supplier invoice or Lightyear total.