Accounting Services for E-Commerce Businesses in Lithuania

AT A GLANCE

E-commerce accounting goes beyond standard bookkeeping — it requires OSS VAT reporting for EU cross-border sales, IOSS for non-EU imports, multi-currency reconciliation, and marketplace fee accounting.
We provide e-commerce accounting from €250/month for companies without a VAT number and from €350/month for VAT-registered businesses — with OSS and IOSS filings included in the VAT-registered retainer.
The quarterly EU OSS return consolidates cross-border B2C VAT for all 27 EU member states into a single filing with VMI — we prepare and submit it as part of the retainer.
IOSS registration and monthly IOSS returns are available as a standalone service for non-EU sellers importing low-value goods to EU consumers.
All additional services — VAT registration, annual reports, employee registration, and statistical reports — are available at fixed fees with full pricing listed on this page.

Accounting for a Lithuanian e-commerce business covers all of the standard obligations — bookkeeping, VAT, payroll, annual statements — plus the e-commerce-specific requirements that standard accounting retainers typically do not include: OSS quarterly returns for EU cross-border B2C sales, IOSS monthly returns for low-value goods imported from outside the EU, multi-currency payment processor reconciliation, and marketplace fee accounting. We provide e-commerce accounting on a fixed monthly retainer from €250/month, with all statutory filings included. OSS and IOSS filings are included in the VAT-registered retainer for e-commerce clients.

Why E-Commerce Accounting Is Different

An e-commerce business that sells to EU consumers across multiple countries, accepts payments through Stripe or PayPal, sources products from Asian suppliers, and operates through Amazon FBA has an accounting profile that is materially more complex than a standard service business with the same revenue. Most general accounting retainers are designed for the latter. We design ours for the former.

Multi-currency and multi-channel transactions

An active e-commerce business typically processes transactions in multiple currencies — GBP, USD, PLN, SEK, and EUR simultaneously — with exchange rate gains and losses arising on every non-EUR transaction. Each payment processor also takes its own fees before remitting — Stripe’s net settlement, Amazon’s marketplace fee and FBA fulfilment cost, PayPal’s transaction charges — meaning the gross sale value and the amount received in the bank are never the same number. Reconciling these across four channels on a monthly basis is a different accounting task from processing a standard bank statement.

OSS and IOSS VAT obligations

An e-commerce company selling to consumers across multiple EU member states must report VAT for each country separately — specifying how much was sold in France at 20%, how much in Germany at 19%, how much in Poland at 23%. The OSS return consolidates this into a single filing, but the underlying data — sales by country at the correct local VAT rate — must be correctly extracted from the payment processor or e-commerce platform records. A standard accountant who has not set up the accounting system to capture country-level sales data cannot produce an accurate OSS return. We configure the accounting setup specifically for OSS compliance before the first sale is made.

Inventory and cost of goods accounting

For e-commerce businesses that sell physical products, inventory accounting adds another layer of complexity. The cost of goods sold must be correctly matched to revenue — which requires tracking stock levels, accounting for supplier invoices in foreign currencies, writing off slow-moving or returned stock, and calculating accurate gross margins. For businesses using Amazon FBA, the FBA inventory held in Amazon’s fulfilment centres in multiple EU countries creates both VAT registration considerations (goods stored in Germany trigger a German VAT registration) and inventory accounting obligations that must be reflected correctly.

Returns and refunds

E-commerce businesses experience significantly higher return rates than physical retailers — particularly for clothing, footwear, and consumer electronics. Every return creates an accounting entry: the revenue must be reversed, the cost of goods must be adjusted, the payment processor fee may or may not be refunded, and the return must be reflected in the VAT return for the correct period. A standard bookkeeper who processes sales invoices but not return credits will produce overstated revenue and incorrect VAT positions within a few months.

What Our E-Commerce Accounting Service Covers

Our e-commerce accounting retainer covers the full statutory accounting cycle plus the e-commerce-specific requirements that apply to cross-border online retail. Every item below is included in the monthly retainer at no additional charge.

Monthly bookkeeping

All transactions are recorded each month under Lithuanian Business Accounting Standards — sales revenue by channel and country, cost of goods sold, payment processor fees, marketplace charges, shipping costs, and operational expenses. Multi-currency transactions are converted at the applicable exchange rate and unrealised FX gains and losses are calculated monthly. Bank reconciliation is performed across all company accounts and payment processor settlements.

Marketplace and payment processor reconciliation

Amazon, Zalando, eBay, Shopify, and similar platforms provide settlement reports that combine gross sales, returns, fees, and net proceeds into a single figure. We reconcile each settlement report back to the underlying transaction data — confirming that every sale, every return, every fee charge, and every currency conversion is correctly recorded. For Amazon FBA sellers, we separately account for FBA fulfilment fees, storage fees, and removal order costs as they appear in the seller account reports.

Lithuanian VAT return

Monthly or quarterly Lithuanian VAT returns are prepared and submitted to VMI. For e-commerce companies, the VAT return includes domestic Lithuanian sales, intra-EU B2B supplies (EC sales declarations), and any reverse charge transactions. The return is filed through the EDS electronic declaration system before the statutory deadline. We notify you of the VAT balance due or refundable before each filing.

EU One Stop Shop (OSS) quarterly return

The OSS return consolidates all cross-border B2C EU VAT into a single quarterly filing. We extract the country-level sales data from your payment processor or e-commerce platform records, apply the correct VAT rate for each EU member state, and prepare and submit the OSS return with VMI by the deadline — the last day of the month following the end of each calendar quarter. We also advise on whether OSS registration is appropriate for your current sales volumes and profile.

IOSS monthly return (where applicable)

If your company is registered for IOSS — either as a non-EU seller importing low-value goods directly to EU consumers, or as an EU seller who sells through your own website and ships from a non-EU warehouse — we prepare and submit the monthly IOSS return. The IOSS return reports all low-value import transactions by EU member state and remits the corresponding VAT through VMI. We also advise on whether IOSS registration is required or beneficial for your specific fulfilment model.

Intrastat declarations

Lithuanian companies that move goods into or out of Lithuania from/to other EU member states above the annual Intrastat threshold must file statistical declarations with Lietuvos statistika. The threshold for arrivals is €280,000 and for dispatches €200,000. For e-commerce businesses that import goods into Lithuania for local stock or ship from Lithuanian stock to EU customers, Intrastat reporting may apply. We assess the threshold and file declarations where required.

Payroll and employer declarations

If the company employs Lithuanian-based staff — warehouse operatives, customer support, or operations managers — monthly payroll is calculated and filed. This includes gross-to-net salary calculation, GPM at 20–32%, employee social contributions (19.5%), and employer contributions (1.77% + 3% health insurance). The GPM313 declaration is filed with VMI and the SoDra employer declaration by the 15th of the following month.

Annual financial statements and CIT return

At the financial year end, we prepare the full set of annual financial statements — balance sheet, P&L, and notes. The annual CIT return is filed with VMI by the 15th of the sixth month after year end. For e-commerce companies with inventory, the financial statements include a closing stock valuation and a cost of goods sold calculation reconciled to the revenue recorded during the year.

Monthly management report in English

Each month we deliver a management report covering: revenue by channel and geography, cost of goods sold, gross margin, operating expenses, net profit, VAT position (Lithuanian + OSS), cash balance, and upcoming filing deadlines. The report is written for operators, not accountants — plain numbers, channel-level performance, and any items that require your attention before the next filing.

OSS and IOSS: How the Filings Work

The EU VAT returns for e-commerce companies — the standard Lithuanian VAT return, the OSS return, and the IOSS return — serve different purposes and cover different transaction types. Understanding which filing covers which sales is the prerequisite for avoiding gaps or double-reporting.

Transaction type	Which return	Filed with	Frequency
Sales to Lithuanian VAT-registered businesses (B2B)	Standard Lithuanian VAT return	VMI	Monthly / quarterly
Sales to consumers in Lithuania (B2C domestic)	Standard Lithuanian VAT return	VMI	Monthly / quarterly
Sales to VAT-registered businesses in other EU states (B2B)	Standard Lithuanian VAT return + EC sales list	VMI	Monthly / quarterly
Sales to consumers in other EU states — goods from LT (B2C)	OSS quarterly return	VMI (via OSS portal)	Quarterly
Digital services to EU consumers from any EU state (B2C)	OSS quarterly return	VMI (via OSS portal)	Quarterly
Low-value goods (≤€150) imported from non-EU to EU consumers	IOSS monthly return	VMI (via IOSS portal)	Monthly
Goods exported from EU to non-EU customers	Zero-rated — standard LT VAT	VMI	Monthly / quarterly

Amazon FBA and local VAT registrationsIf your company stores goods in Amazon FBA fulfilment centres located in other EU member states — Germany, France, Poland, Czech Republic, for example — those goods are considered to be held in stock in those countries. This creates a VAT establishment in each storage country, requiring a local VAT registration separate from OSS. OSS does not cover sales from local stock — it only covers cross-border sales dispatched from the company’s home country. For Amazon FBA sellers using Pan-European FBA, local VAT registrations in each FBA country are typically required. We advise on this before you activate Pan-European FBA.

E-Commerce Accounting Prices

All accounting services are priced at fixed monthly retainers for ongoing work and fixed fees for one-off engagements. There are no hourly charges, no surprise invoices, and no additional fees for routine OSS and IOSS filings within the scope of the retainer.

Monthly retainer options

Accounting Service — Company Without VAT Number · Standard

from €250 / month

Monthly bookkeeping under Lithuanian accounting standards
Multi-currency bank and payment processor reconciliation
Quarterly advance CIT payments — calculated and filed
Annual financial statements — balance sheet, P&L, notes
Annual corporate income tax return
JAR annual data confirmation
Monthly management report in English — revenue, margin, cash

Accounting Service — Company With VAT Number · Standard + VAT

from €350 / month

Everything in the non-VAT package, plus:
Monthly or quarterly Lithuanian VAT return — including EC sales declarations
EU OSS quarterly return — cross-border B2C VAT for all EU member states
IOSS monthly return — where the company is IOSS-registered
Intrastat declarations — where the company meets the reporting threshold
Input VAT reclaim on eligible business purchases
VAT and OSS position summary in the monthly management report

What determines the final monthly feeStarting rates apply to companies with low-to-moderate transaction volumes. The monthly retainer is fixed based on the number of transactions processed — sales, returns, supplier invoices, payment processor settlements, and IOSS line items. We assess your expected volume at onboarding and set a fixed monthly rate. The rate is reviewed as volumes grow — always a fixed amount, never hourly.

Additional Services and Fixed Fees

The following services are available outside the monthly retainer at fixed fees. These cover one-off registrations, periodic filings, and specialist services that not every e-commerce business needs every month.

VAT and registration services

Service	Price
Assistance registering VAT number (for residents)	€800
Assistance registering VAT number (for non-residents)	€1,500
EU OSS registration with VMI One-off registration for the One Stop Shop scheme	€400
IOSS registration with VMI One-off Import One Stop Shop registration for non-EU sellers	€500
Local VAT registration in another EU country Required for FBA sellers storing goods in other EU member states	On request
Annual report for a Lithuanian company	from €650
Individual tax consultation	from €300
Winding up a Lithuanian company	from €850

Per-item and ad hoc services

Service	Price
Accounting of additional primary documents Sales, purchase invoices from companies or individuals in any currency	€7 / invoice
Accounting of bank transaction in any currency	€1 / transaction
Employee registration in Social Insurance Fund (SoDra)	€50 / person
Wage calculation for additional employee Admission, dismissal, vacation, maternity, unpaid leave, declarations	€70 / month
Accounting for fixed assets	€30
Other work unspecified in contract	€120 / hour
Urgent work fee Applied to base invoice for urgent requests	50% surcharge

Getting Started: E-Commerce Accounting Onboarding

We onboard new e-commerce accounting clients within 5–7 business days. The onboarding process is structured to ensure the accounting system is correctly configured for your sales channels, VAT obligations, and product type before the first transaction is recorded.

Initial call and scope confirmationWe discuss your e-commerce channels (own website, Amazon, Zalando, etc.), product categories, the countries you sell to, whether you ship from Lithuania or a non-EU warehouse, your current transaction volumes, and your VAT registration status. We confirm the retainer tier, identify any OSS or IOSS registration needs, and confirm whether any local EU VAT registrations are required (e.g., for FBA countries).

Accounting system configurationWe configure the chart of accounts and revenue tracking structure for your sales channels and geographies. For multi-channel businesses, we set up separate revenue categories for each channel so the management report shows performance by platform. We also configure the OSS data capture — ensuring country-level consumer sales data is extracted correctly from each platform for the quarterly OSS return.

VAT registrations (if needed)If the company is not yet VAT-registered with VMI, we file the registration application. If OSS or IOSS registration is needed, we complete those simultaneously. For FBA sellers who need local VAT registrations in other EU member states, we advise on the correct approach and, where required, introduce local fiscal representatives.

Payment processor and marketplace integrationWe confirm the format and frequency of settlement reports from each of your payment processors and marketplaces — Amazon Seller Central, Stripe Dashboard, Shopify Payouts, etc. — and set up the data flow into the accounting system. For high-volume businesses, we can automate the import of transaction data; for lower-volume businesses, monthly report uploads are sufficient.

Prior period catch-up (if needed)If the company has been trading without accounting records, or if the prior accountant’s records need to be reviewed, we scope and cost the catch-up project before starting. For e-commerce businesses with unreported OSS obligations, we advise on the voluntary disclosure approach with VMI to regularise the position before it becomes the subject of an audit.

Monthly cycle beginsFrom the first full month, the accounting cycle runs to a defined schedule. Settlement reports and invoices arrive at agreed intervals, we process and reconcile, and the management report — with Lithuanian VAT, OSS position, and IOSS summary where relevant — is in your inbox by the 15th of the following month.

Frequently Asked Questions

Yes — the quarterly EU OSS return is included in the VAT-registered e-commerce accounting retainer at no additional charge. Preparing the OSS return requires country-level sales data extracted from your payment processor or marketplace reports. We configure the accounting system to capture this data at setup so the OSS return can be produced directly from the accounting records each quarter. If you currently have a VAT-registered company but are not yet registered for OSS, we handle the OSS registration as a one-off service at €400 and then include future filings in the retainer.

IOSS applies to sellers of goods with a value below €150 imported from a non-EU country and sold directly to EU consumers. If you ship products from China, the UK, or another non-EU warehouse to EU consumers through your own website, IOSS registration allows you to collect VAT at the point of sale and remit it through VMI — avoiding the buyer being charged import VAT at the border. IOSS does not apply to goods already in the EU, goods above €150, or goods sold through a marketplace that handles IOSS on your behalf. We assess whether IOSS registration is right for your fulfilment model and register the company for IOSS at €500 as a one-off service, with monthly IOSS returns included in the VAT-registered retainer thereafter.

Almost certainly yes. When Amazon stores your goods in a fulfilment centre in Germany, Poland, France, or another EU country, you are deemed to hold stock in that country — which creates a VAT presence there and requires a local VAT registration. OSS does not cover sales dispatched from another country’s stock. This is one of the most common and most expensive compliance gaps for FBA sellers. We advise on which countries require local registration based on your FBA inventory report and introduce fiscal representatives in each country where needed. Local VAT registration assistance is quoted on request as it varies by country.

Returns and refunds are accounted for in the month they are processed — the revenue is reversed, the VAT is adjusted in the applicable return (Lithuanian VAT, OSS, or IOSS depending on the original transaction), and if the goods are returned to stock, the inventory value is updated. For marketplace sellers, return-related adjustments appear in the settlement reports which we reconcile monthly. For companies with high return rates, we track returns as a separate metric in the management report so you can monitor the true net revenue position by channel.

Intrastat is a statistical reporting obligation for companies that move goods between EU member states above specified annual thresholds. In Lithuania, the threshold is €280,000 for arrivals (goods coming into Lithuania from other EU states) and €200,000 for dispatches (goods leaving Lithuania to other EU states). If you import goods from an EU supplier into Lithuania for your stock, or ship goods from Lithuanian stock to business customers in other EU states, you may meet the Intrastat threshold. The reporting is statistical — it does not affect VAT — but it is a legal obligation and late or missed filings attract administrative fines. We monitor the threshold and file Intrastat declarations where required as part of the retainer.

Yes, but it requires a voluntary disclosure process with VMI and potentially with the tax authorities of the EU member states where you had unreported VAT obligations. The exact process depends on how long the non-compliance has been ongoing and which countries are affected. We advise on voluntary disclosure as part of the OSS registration engagement — assessing the extent of the historic liability, advising on the most practical approach to regularisation, and handling the correspondence with VMI. Voluntary disclosure, while uncomfortable, is significantly less costly than an audit discovery of the same liability.

Yes. Drop-shipping creates specific accounting and VAT questions — particularly around whether the Lithuanian company is acting as principal (buying and reselling goods) or as agent (arranging the sale on behalf of the supplier). The answer affects revenue recognition, VAT treatment, and customs documentation. For drop-shipping from non-EU suppliers to EU consumers, IOSS may also apply. We assess the correct accounting and VAT treatment for the specific drop-shipping model before setting up the accounting system — ensuring the books correctly reflect the economic substance of the transactions.

Ready to set up e-commerce accounting?

Contact us with details of your sales channels, product categories, and current VAT status. We will confirm the correct retainer, assess OSS and IOSS registration needs, and begin the onboarding process within 48 hours of your instruction.