How to check purchases against e-Fatura

What is it for?

Check against e-Fatura compares, in one step, the file of your purchases downloaded from the e-Fatura Portal with the supplier invoices you have in the accounts, and tells you which are missing on each side. For those the AT knows about and the accounts do not have, it prepares a draft invoice.

Nothing is sent to the AT: fiscaldoo never connects to the Portal das Finanças. You download the file and load it here.

When to use it?

• Before closing VAT, to catch purchases a supplier communicated to the AT that you have not entered yet.
• At year end, to check that everything in e-Fatura is in the accounts (and the other way round).
• It is not the same as importing the file: How to import invoices from e-Fatura stores the Portal's documents and follows each one until it is entered. This check is a quick comparison that is not saved.

Where to find it?

• Accounting › Reconcile › Banks and cash › Check against e-Fatura, with the Accountant profile (or Fiscal officer).
• Audit › Checks › Purchase documents check, with the Auditor or Fiscal officer profile: the report that cross-checks supplier invoices with the documents imported from e-Fatura (see step 7).

Before you start

• The Copilot must be switched on for the company, with the “Check against the e-Fatura file” switch. They are switched on by the Fiscal administration profile (in the example, the administrator), in Copilot › Control › Switches, with the company chosen in the top right corner: switch on Copilot (master switch of the company) and Check against the e-Fatura file. This check is “safe”: it only compares data you already have and does not use artificial intelligence.
• You have the purchases list file from the e-Fatura Portal, in CSV or XLSX. Pending validation on screen: the export path in the Portal das Finanças and the exact column titles of the 2026 file (the demo does not connect to the real AT; the example file was written by hand, with columns the screen recognises).
• The example is Empresa Demonstração, Lda, with the purchases of September 2026. The file has 7 invoices, from 02/09/2026 to 28/09/2026, with the columns NIF Emitente, Nome Emitente, Tipo Documento, Número Documento, Data Documento, Valor IVA and Total.

How to use it

1. Open Accounting › Reconcile › Banks and cash › Check against e-Fatura. The Check against the e-Fatura file form opens, with the e-Fatura file (CSV or XLSX) field.
2. Click Choose a file and choose the file.
3. Click Compare. The screen reads the file and counts: File: 7 invoices from 02/09/2026 to 28/09/2026; In both places: 5; The AT knows and the accounting does not have: 2; The accounting has and the AT does not know: 1; and 1 bills of suppliers without a Portuguese NIF were left out (the invoice of a US supplier, which the AT does not know).
4. Read the table. Only the differences appear:
   • The AT knows it, the accounting does not have it (in orange): FT SC/2026/77 from Serralharia do Cávado, Lda (369,00 €) and FT PAP/2026/131 from Papelaria Central, Lda (123,00 €). Each line has Create the draft.
   • The accounting has it, the AT does not know it (in blue): FT EML/2026/45 from Equipamentos e Mobiliário Lusitano, Lda (246,00 €), with Open the bill. It may be an invoice the supplier did not communicate, or one of your invoices with a number or date different from the Portal; ask the supplier to confirm.
5. For a missing invoice, click Create the draft. The Draft vendor bill opens with the supplier (if the NIF does not exist, it creates it), the Bill Reference equal to the document number, the Bill Date (17/09/2026), the Purchases journal and a single line with the total (369,00 €, account 6228 Outros, no VAT and no VAT deduction). The chatter records: “Draft prepared by the Copilot from the e-Fatura file: only the total is known. Complete the taxes and the account and confirm it yourself.”
6. Complete the draft before you confirm it: split the amount into base and VAT (in this example, 300,00 € plus 69,00 €), choose the right expense account and check the Accounting Date (30/09/2026 in this example), which decides the VAT period. The step by step is in How to enter a supplier invoice. Once the draft is created, comparing the same file again gives In both places: 6 and only one missing invoice is left (FT PAP/2026/131). A draft already counts as “in both places”: the check does not prove the invoice was confirmed.
7. For the whole-year picture, the Purchase documents check report (Audit › Checks) lists each supplier invoice with e-Fatura: matched or e-Fatura: not found in the imported file. It only knows what was imported through the Record › Import menu (see the article on importing): in the example, after importing the 6 September invoices, the September ones with the same NIF and number were “matched” and all the others “not found”, even the legitimate ones. This report does not use this check's file.

Expected result

• A list with only the differences, one line per invoice, and the count of what is in both places.
• The draft of each missing invoice, waiting to be confirmed. The invoice only enters the accounts when you confirm it.

Important notes

• An invoice is “in both places” if it has the same supplier NIF and the same document number (spaces and signs do not count), or, without an identical number, the same NIF, the same date and the same total (0,01 € tolerance). The total is not checked when the number is the same: in the example, FT TEL/912 came in the file with 120,00 € and is in the accounts with 116,85 €, and the screen counted it as “in both places” without a warning. Check the amounts in the purchases report or on the invoice.
• It only compares invoices in the accounts dated within the file's period (from the oldest to the most recent date in the file). A September file does not detect what is missing in October.
• It does not know invoices from foreign suppliers (the AT does not have them): they are left out and the screen says how many. Nor cancelled invoices.
• The draft only keeps the total: no VAT, no deduction and account 6228. Do not confirm it without completing it. Pending validation by a certified accountant: the VAT deduction of invoices created by this check (the screen shows 0,00 € of deductible VAT until you complete them).
• Credit notes. Supplier credit notes you have in the accounts enter the comparison like any invoice: if the file has no line with the same NIF and number, they appear under “The accounting has it, the AT does not know it”. What the screen does not see is the document's status on the Portal (for example, cancelled). Pending validation on screen: how the check handles credit-note lines in the file itself.
• Anyone who cannot switch on the Copilot (for example, a Fiscal officer who is not Fiscal administration) gets the message and cannot run the check.

Common problems

“The Copilot is turned off for the company”

• Cause: the master switch or the check's switch is off for the company.
• What to do: ask the Fiscal administration profile to switch them on in Copilot › Control › Switches. The screen message says: “The Copilot is turned off for company "Empresa Demonstração, Lda". Nothing was done. Only the Fiscal administration profile can turn on the Copilot and this agent: ask someone with that profile.”

“Choose the file you downloaded from the e-Fatura Portal (CSV or XLSX)”

• Cause: you clicked Compare without choosing the file.
• What to do: choose the file and compare again.

“The file has no usable invoice line”

• Cause: the file only has the title row (or the rows are empty).
• What to do: check that the list you downloaded has purchase invoices.

“The columns of the file were not recognised”

• Cause: the column titles are not the ones the screen knows (tested with Emissor, Referência, Dia and Montante). The screen opens a window that gives the format read, the file's columns and what is still missing.
• What to do: in the four boxes Column of the supplier NIF, Column of the document number, Column of the document date and Column of the total, type the title of the matching column in your file, click Save and then Compare. In the example, with the four titles, the screen compared the file's single line (“In both places: 1”). The message uses technical names (supplier_vat, document_number, document_date, total_amount) for what is missing: in order, the NIF, the number, the date and the total.