The short answer
Prepare i.SAF registers and FR0600 as related but separate outputs. Confirm each reporting period, reconcile the underlying records and explain differences before submission. Track review, acceptance and payment separately; a technically accepted file does not prove that its accounting treatment is correct.
Confirm the period before copying last month's task
For a Lithuanian legal entity, do not assume the FR0600 period and i.SAF period are identical. Record the client's actual VAT period and its effective date. VMI publishes separate rules for FR0600 filing and i.SAF register submission. Both pages were checked on 6 October 2026.
A firm with 30 clients needs an obligation list, not 30 identical copied checklists. Keep client, period, preparer, reviewer, document cut-off and filing status together. When VAT registration or reporting frequency changes, update future work and inspect any already-created task before the next filing.
Collect documents with the reconciliation in mind
Request sales invoices, purchase invoices, credit notes and any relevant transaction evidence by period. Ask about foreign purchases, marketplace activity and unusual transactions explicitly. A bank statement helps identify gaps but is not a substitute for the invoice or the accountant's VAT assessment.
Collection and preparation
Collection and preparation
- Confirm all bank accounts and sales channels used in the period.
- Check invoice sequences, duplicates and cancelled documents.
- Record missing documents individually, with an owner and next action.
- Review credit notes, foreign transactions and period cut-off.
- Resolve tax classification in the accounting system before exporting.
Explain differences instead of forcing matching totals
An invoice-register total is not automatically the figure that belongs in every VAT-return field. Timing, non-deductible VAT and transactions outside the invoice register can create differences. Build a reconciliation that starts with the ledger, identifies relevant register totals and explains each adjustment. Investigate a difference rather than changing numbers merely to make the two reports agree.
Illustrative review notes
| Observation | Question | Evidence to keep |
|---|---|---|
| Duplicate supplier invoice | One transaction or two different invoices? | Invoice number, supplier and original file |
| Credit note received later | Which period and treatment apply? | Original invoice, credit note and decision |
| Foreign service purchase | Which VAT treatment and reporting fields apply? | Supplier details and transaction analysis |
| Ledger/register difference | Timing, classification or missing data? | Reconciliation with reviewer approval |
For example, a €210 difference is an investigation item, not permission to add €210 to a return. Identify the transaction, confirm the treatment and make an authorised correction in the ledger if needed. Preserve the earlier export so the reviewer can see what changed.
Review, submit and confirm as distinct steps
Agree who can prepare, approve and submit. A technically valid export still needs accounting review. After submission, inspect the authority's processing result and retain the acknowledgement, version and period. Uploading a file and seeing a success banner in another tool does not prove the authority accepted the final register or return.
Track payment separately: who tells the client the amount, who initiates it and what evidence closes the task. For a rejected filing, leave the work open, assign the error and set the next check. Do not count a rejected attempt as a completed obligation.
Keep late invoices out of an invisible side process
If a document arrives after submission, record its receipt date and affected period. A reviewer decides whether a correction is necessary under the applicable rules. Keep the correction linked to the original filing; otherwise the next accountant sees two exports and no explanation. See the late-document process for the operational handoff.
Put the approved sequence into recurring work, use the i.SAF review checklist before release and the Lithuania calendar for due-date planning. Claister can keep tasks and document requests on a client's record. It does not decide VAT treatment or file declarations for the firm.
Questions
Do not impose a blanket equality. Reconcile the relevant figures and explain legitimate differences using the ledger and the rules for the actual transactions.
No. Export, review, submission and acceptance are different checkpoints. Keep the authority's acknowledgement for the final version.
About this article
Author: Claister
Published by Claister, the company building the accounting practice management software discussed on this website.
Design partner: Natalija Miadzelic
Tax review: Natalija Miadzelic · Accountant · Approved
Consulting an official source is separate from a qualified review of how a rule applies to a particular client.
Editorial policySources cited in this article
- FR0600 filingPage consulted ·
- i.SAF register submissionPage consulted ·
Dates below describe recorded source consultation, not professional approval. Sources without a recorded date are listed without one.
Accounting processes: monthly work to annual accounts
Related tools, workflows and product guides
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