Our Complete VAT Services
Our VAT experts handle every aspect of Estonian VAT management — from registration and periodic filings to VAT refunds, corrections, and communication with the Tax and Customs Board.
Whether you operate an e-commerce store, offer digital services across the EU, or manage cross-border trade, we ensure your VAT reporting is accurate, timely, and optimized for your business model.
With over 10 years of experience in Estonian and EU VAT compliance, we make complex tax processes straightforward and stress-free.
- VAT Registration and Deregistration in Estonia
- Monthly and Quarterly VAT Return Preparation
- Intra-Community VAT Compliance
- VAT Reclaim Services
LKS Consult
All-in-One VAT Services
VAT Registration and Deregistration in Estonia
When Do You Need VAT Registration?
- Your taxable turnover exceeds €40,000 in a calendar year
- You provide services to EU businesses (reverse charge mechanism)
- You sell goods or services requiring immediate VAT registration
- Voluntary registration for VAT reclaim purposes
Our VAT Registration Services:
- Eligibility assessment – determining if and when you need to register
- Application preparation – completing all required forms and documentation
- Submission to Tax and Customs Board – handling the entire registration process
- VAT number receipt – typically within 3-5 business days
- Post-registration setup – configuring your accounting for VAT compliance
VAT Deregistration Support:
- Assessment of deregistration eligibility
- Preparation and submission of deregistration application
- Final VAT return preparation
- Outstanding VAT settlement
- Communication with tax authorities
Timeline: VAT registration typically takes 3-5 business days after submission. We handle the entire process from start to finish.
Monthly and Quarterly VAT Return Preparation
Estonian VAT returns must be submitted by the 20th day of the month following the reporting period. Late submissions result in automatic penalties starting from €32.000 + daily interest of 0.06%
Our VAT Return Services Include:
Data Collection and Verification:
- Review of all sales invoices (output VAT)
- Analysis of purchase invoices (input VAT)
- Verification of VAT rates applied (0%, 9%, 13%, 24%)
- Identification of exempt and out-of-scope transactions
- Cross-border transaction validation
VAT Calculation and Reporting:
- Accurate calculation of VAT payable or refundable
- Preparation of VAT return (KMD INF form)
- Annex 1: Intra-Community supply of goods
- Annex 2: Acquisitions and supplies of goods with installation
- Annex 3: Services under reverse charge mechanism
- Annex 4: E-services, telecommunications, and broadcasting
Submission and Payment:
- Electronic submission to Tax and Customs Board
- Payment calculation and instructions
- Confirmation of successful submission
- Digital archive of all submitted returns
Return Frequency:
- Monthly returns: For most VAT-registered businesses
- Quarterly returns: Available for businesses with turnover under €200,000
- We recommend the optimal frequency for your situation
Intra-Community VAT Compliance
Doing business within the EU requires special VAT treatment and reporting. We ensure full compliance with intra-community VAT rules.
Intra-Community Supply of Goods:
- Zero-rated VAT verification (0%)
- Customer VAT number validation via VIES system
- Proper documentation and proof of transport
- Recapitulative statements (summary reports)
- Intrastat declarations (if applicable)
Intra-Community Acquisition of Goods:
- Estonian VAT application on goods purchased from EU
- Reverse charge mechanism application
- Simultaneous input VAT deduction (when applicable)
- Proper recording in VAT returns
Services to/from EU Businesses:
- B2B service rules application
- Reverse charge documentation
- Place of supply determination
- VAT exemption verification for qualifying transactions
EC Sales Lists (Recapitulative Statements):
- Monthly submission of intra-community supplies
- Customer VAT number reporting
- Value declaration by member state
- Deadline: 20th day of following month
VAT Reclaim Services
Did you pay VAT that you can reclaim? We help you recover VAT paid on business expenses.
Estonian VAT Reclaim:
- Review of all business expenses for VAT recovery
- Identification of reclaimable VAT amounts
- Proper documentation and substantiation
- Input VAT claims in monthly returns
- Maximizing your VAT refunds
Foreign VAT Reclaim: For VAT paid in other EU countries:
- Assessment of reclaimable foreign VAT
- Application preparation for each EU country
- Submission through Estonian Tax Board portal
- Follow-up on claims and communications
- Recovery of VAT refunds from EU member states
Refund Timeline:
- Estonian VAT: Typically refunded within 30 days
- EU VAT: Can take 4-8 months depending on the country
Commonly Reclaimable VAT:
- Office supplies and equipment
- Business travel and accommodation
- Professional services (legal, consulting)
- Marketing and advertising
- Software and subscriptions
- Vehicle expenses (with restrictions)
Ready to start?
Leave us request and we will make proposal
Creating Success
Why Choose LKS Consult for VAT Services in Estonia?
Whether you’re a small business owner seeking guidance on tax optimization, a startup in need of comprehensive financial planning, or a large corporation looking for strategic financial insight, our team of accountants is here to support you every step of the way.
Deep Estonian and EU VAT Expertise
VAT regulations are complex and constantly evolving.
Our team:
Stays updated on all Estonian VAT changes
Monitors EU VAT directive implementations
Understands cross-border VAT complications
Has handled thousands of VAT returns successfully
Navigates audits and disputes with tax authorities
Zero Penalties, Perfect Timing
We've never missed a VAT deadline for our clients. Our systematic process ensures timely submission every time.
E-Commerce and Digital Business Specialists
Special expertise in:
OSS scheme implementation and management
Digital product and service VAT treatment
Marketplace seller obligations
Dropshipping VAT compliance
Cross-border e-commerce structures
Proactive VAT Optimization
We don't just submit returns—we optimize your VAT position:
Identify opportunities for VAT recovery
Recommend optimal business structures for VAT efficiency
Advise on VAT-exempt vs. taxable activities
Suggest timing strategies for cash flow improvement
Plan for major purchases or investments
Multilingual VAT Support
VAT services in Estonian, English, Russian, and Spanish:
Clear explanations of complex VAT concepts
Communication with Estonian Tax Board on your behalf
Translation of VAT-related documents
Support for international teams
Full Audit Support
If the Tax and Customs Board initiates a VAT audit:
We represent you throughout the process
Provide all necessary documentation
Handle all communications with auditors
Explain and defend VAT positions
Resolve disputes and discrepancies
Tax
Estonian VAT:
Essential Information
Key VAT Rules
- Invoicing: VAT invoices must include specific information
- Record keeping: All VAT documents must be kept for 7 years
- Place of supply: Different rules for goods vs. services
- Reverse charge: Applies to specific transactions
VAT Rates in Estonia (2025)
Standard rate: 24% (most goods and services)
Reduced rate: 9% & 13%(books, publications, certain services, accommodation)
Zero rate: 0% (intra-community supplies, exports outside EU)
Exempt: No VAT charged (certain healthcare, education, financial services)
VAT Registration Threshold
Mandatory: €40,000 turnover in a calendar year
Voluntary: Can register below threshold for VAT reclaim purposes
VAT Return Deadlines
Submission: 20th day of the month following the reporting period
Payment: Same day as submission (20th)
OSS: Last day of the month following the quarter
FAQs about payroll services in Estonia
You must register if:
- Your annual turnover exceeds €40,000
- You provide reverse charge services to EU businesses
- You acquire goods from other EU countries
You may voluntarily register below the threshold if you want to reclaim input VAT.
If you miss the VAT deadline in Estonia, you’ll be charged interest of 0.06 % per day on any unpaid tax. The Tax and Customs Board may also impose a fine for late or incorrect submission—typically up to €1,300 for the first notice and €2,000 for repeat cases. Repeated delays or non-compliance can also increase your audit risk.
Yes, but with limitations. You can reclaim VAT on goods and services purchased up to 6 months before registration, provided they’re still used in your business and you have valid invoices.
- 0% VAT: You charge 0% but can reclaim input VAT (e.g., exports, intra-EU supplies)
- VAT-exempt: No VAT charged and you cannot reclaim input VAT (e.g., healthcare, education)
This distinction significantly impacts your business costs
- Standard: 30 days from return submission
- Large refunds: May take up to 90 days with additional verification
- Foreign VAT: 4-8 months depending on the EU country
We follow up on all refund claims to ensure timely payment.
Essential documents include:
- All sales invoices issued
- All purchase invoices received
- Bank statements
- Contracts for services
- Proof of delivery for goods (especially cross-border)
- Customer VAT numbers for B2B EU sales
We provide guidance on proper document retention and organization.
Yes, if your turnover is below €200,000 annually. The change typically takes effect from the beginning of the next calendar year. We can submit the application for you.
This creates complex VAT scenarios because:
- Goods and services have different place-of-supply rules
- B2B and B2C sales are treated differently
- Different VAT rates may apply
We analyze your specific situation and ensure correct VAT treatment for each transaction type.
It depends on:
- What you sell (goods vs. services)
- Who you sell to (B2B vs. B2C)
- Sales volumes in each country
- Whether you have physical presence
OSS often eliminates the need for multiple registrations. We assess your situation and recommend the optimal structure.
- Keep in mind that accounting regulations and requirements may change over time, so staying informed and seeking professional advice when necessary is crucial to ensure compliance and financial success in Estonia.
