VAT Registration, Transfer & Deregistration for Pharmacies (UK)
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30+ years of experience
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Specialised Pharmacy VAT Expert in UK
What does our end-to-end service include?
You get an end-to-end, pharmacy-specific VAT service led by a VAT accountant and VAT consultant team that understands NHS timing, EPOS mapping, and partial exemption.
Scope of work
- Registration, number transfer, deregistration
- Threshold monitoring and advice on early registration when input VAT recovery is material.
- Preparation and submission of VAT1, agent authorisation, and HMRC correspondence.
- Transfer of registration and TOGC assessment on takeovers, with HMRC notifications and target-date planning.
- Deregistration planning, final return, and deemed supply checks on stock and assets.
- Threshold monitoring and advice on early registration when input VAT recovery is material.
- System setup and MTD compliance
- Xero configuration with pharmacy VAT codes across 20%, 5%, 0%, exempt and outside scope.
- Digital capture setup in Dext or Hubdoc for invoices, credit notes, and group rebates.
- EPOS and till VAT mapping for OTC, contraception at 5%, zero-rated medicines, and exempt services.
- Xero configuration with pharmacy VAT codes across 20%, 5%, 0%, exempt and outside scope.
- Monthly and quarterly compliance
- NHS PPD accruals and timing reconciliations.
- Supplier rebates, buying group commissions, and credit notes posted with correct VAT reversal logic.
- Import VAT via PIVA captured and reconciled.
- Partial exemption calculations and monitoring with annual true-up.
- NHS PPD accruals and timing reconciliations.
- Ownership change and multi-branch design
- Single registration, divisional records, or VAT group design with governance and control.
- Day-one continuity plan for suppliers, NHS payments, EPOS, and bank feeds.
- Single registration, divisional records, or VAT group design with governance and control.
- Governance, evidence and HMRC defence
- Entry-by-entry audit trail in Xero aligned to MTD.
- VAT working papers for each period, including DGT summaries and retail adjustments where relevant.
- HMRC enquiry handling, penalty mitigation, and time-to-pay support.
- Entry-by-entry audit trail in Xero aligned to MTD.
Your deliverables
- VAT onboarding checklist tailored to your branch mix, NHS profile, and systems.
- Periodic VAT reconciliation pack covering PPD, EPOS, supplier credits, rebates and import VAT.
- Annual partial exemption and retail scheme adjustment workbook.
- Final VAT return pack on deregistration or transfer date.
What will you get from this service?
Clients see clear outcomes that improve compliance, cash flow and operational control.
Faster Refund
Faster refunds and stable cash flow by aligning NHS PPD accruals, EPOS outputs and supplier credits, so monthly VAT reclaims are accurate and timely.
HMRC Compliance
Lower risk of HMRC issues through correct coding, partial exemption control and complete working papers that withstand reviews.
Synchronisations
Seamless takeovers with VAT number transfer or new registration completed on time, so trading continues without supplier or NHS disruption.
Deregistrations
Right-first-time deregistration with final return, deemed supplies, and annual adjustments wrapped up cleanly.
Error Free VAT Return
No double counting because the marginal rate result is reconciled to the retail scheme and partial exemption.
Operational Flexibility
Less admin as we deliver a repeatable month-end pack your team can file under MTD with confidence.
Buying or Selling a Pharmacy? Don’t Let VAT Stall the Deal
Ownership changes are the highest-risk moments for VAT compliance. Whether you are transferring a VAT number via TOGC or starting a fresh registration, we ensure day-one continuity for your NHS payments and supplier accounts.
Contact Information
Who needs to register for VAT and when?
Pharmacies must register when the rolling 12-month taxable turnover exceeds £90,000 or when early registration improves input VAT recovery and credibility. If you expect to cross the limit soon, apply early to avoid back-dated VAT and penalties.
What counts toward the threshold
- Taxable sales at 20%, 5% and 0%.
- Exempt supplies do not count toward the threshold but drive partial exemption.
How we help
- Rolling threshold monitoring and forecasts.
- VAT1 preparation, submission and HMRC queries handled by your VAT accountant.
- MTD-ready setup so you are compliant from the first return.
What information do you need for a smooth VAT registration?
Pharmacies should prepare entity, identity, and trading evidence now to prevent HMRC delays.
Essentials
- Legal structure, Companies House details, directors or partners.
- Trading start date, pharmacy contract details, and turnover split across NHS, private and OTC.
- Bank confirmation, historic VAT numbers if any.
- EPOS VAT map and supplier list for accurate code setup.
MTD and software
- Xero with pharmacy VAT codes and partial exemption tracking.
- Dext or Hubdoc for digital records and audit trail.
How do VAT number transfers work when you buy another branch?
Pharmacies can use a Transfer of a Going Concern to keep continuity and avoid VAT friction when acquiring a branch, provided TOGC conditions are met.
When a transfer is suitable
- You acquire a trading pharmacy and want to keep the VAT number for continuity with NHS and suppliers.
- You move a business into a company structure and need to preserve VAT history.
What we manage
- TOGC eligibility review including property, assets, and stock.
- HMRC notifications within deadlines.
- Xero, EPOS and supplier updates so day-one trading proceeds without interruption.
What if you open, merge, or add multiple branches?
Pharmacies should choose a registration model that matches growth and control requirements.
Options
- Single registration with branch-level tracking.
- Divisional records under one VAT number.
- VAT group for entities under common control to simplify intercompany VAT.
Implementation
- Chart of accounts and tracking categories by branch.
- Consistent EPOS VAT rate logic across sites.
- Standard month-end close covering PPD, rebates and import VAT.
How do you deregister VAT when selling or closing a branch?
Pharmacies must deregister within 30 days when taxable trading stops or expected turnover falls below the deregistration threshold. A clean final return protects you from future queries.
Steps
- Confirm cessation or TOGC date.
- File the final return and account for stock and assets where required.
- Reconcile NHS PPD, OTC DGT, rebates and credits up to the final date.
- Cancel MTD obligations and direct debit after the final submission.
Adjustments
- Deemed supply on stock and fixed assets where input VAT was reclaimed.
- Final partial exemption and any retail scheme annual adjustments.
What pharmacy-specific pitfalls should you avoid?
Pharmacies reduce errors by treating VAT as a control process, not a back-office chore.
Common risks
- Wrong EPOS VAT codes on OTC, contraception at 5%, zero-rated medicines and exempt services.
- Missing partial exemption rules that overstate input VAT recovery.
- Supplier rebates and credit notes posted without reversing VAT correctly.
- PPD timing not accrued, creating refund gaps and HMRC questions.
- Keeping or changing a VAT number when the legal facts do not support it.
Controls we implement
- EPOS VAT map testing with sample transactions.
- Monthly reconciliation pack with clear sign-offs.
- Annual partial exemption and retail adjustments built to HMRC standards.
What happens next?
Pharmacies can book a short discovery call with a VAT expert to confirm whether you need a new registration, a VAT number transfer under TOGC, or a deregistration, and to receive a tailored checklist for your branch and systems. If you prefer, send your last three PPD statements and a sample of supplier invoices and we will map your VAT position and provide a clear plan.
RX Virtual Finance LTD — your pharmacy-specialist VAT accountant, VAT consultant and VAT expert for registrations, transfers and deregistrations with MTD-ready systems and pharmacy-specific reconciliations.
