Bonded warehouse software is a warehouse management system that tracks the duty status of every lot, pallet and receipt, keeps duty-suspended stock separate from duty-paid stock, and records each movement in a form HMRC can check. A bonded warehouse is an HMRC-approved, secure site where goods can be held before the duty on them is paid, so the software has to know the status of every item at all times, not only when stock leaves the building.
This guide sets out what that software has to do, which HMRC records it needs to support, and where a warehouse management system helps and where it does not. It is general information based on HMRC’s published guidance, not legal or tax advice. Check the notices that apply to your goods with HMRC or a customs adviser.
What is a bonded warehouse?
A bonded warehouse is an approved, secure site where goods liable to duty can be stored without paying that duty until they are released or leave the warehouse. HMRC describes an excise warehouse as a place of security approved by HMRC where goods liable to excise duty can be stored without payment of the duty for as long as they remain there. Approval itself is covered in Excise Notice 196, which also says what an operator must show before HMRC will authorise a warehouse.
There are two regimes, and they use different paperwork. Excise warehouses hold goods such as alcohol and fuel, and their rules sit in HMRC’s excise notices. Customs warehouses hold non-UK goods that may still owe customs duty when they are released, and HMRC’s guidance on managing a customs warehouse covers them. Which regime applies depends on what you store, and that decides the software you need.
What bonded warehouse software needs to do
Bonded warehouse software needs to hold a duty status against every piece of stock, stop goods of one status being used to fill an order for another, calculate duty when stock leaves bond, and keep a timestamped record of every movement. Spreadsheets can hold a version of this for a handful of lines, but they cannot stop the wrong pallet being picked on a busy floor. The table below sets out what to test for in any system, with Clarus’s position as shown on its bonded feature page at the time of checking.
| Requirement | What to ask a vendor | Clarus position |
|---|---|---|
| Duty status at goods-in | Can status be recorded when stock is received? | Yes. Whether duty is paid is recorded at receipt. |
| Mixed status for one product | Can bonded and duty-paid stock of the same product sit in the system together? | Yes. Status is tracked per receipt, lot or pallet. |
| Blocking invalid moves | Does the system stop a movement that breaks status rules? | Yes. The system prevents invalid movements. |
| Duty calculation | Where are duty rates held, and when are they applied? | Rates sit on the product record and apply at movement. Historic movements keep the logic they were calculated with. |
| Audit trail | What is recorded for each movement? | Timestamp, user, device, quantity, location and the status decision. |
| HMRC reporting | Does the system submit to HMRC directly? | Weekly HMRC-ready outputs are exported for you to submit. Direct integration is on the roadmap. |
| Product scope | Which goods does the system cover today? | Wet bonded (alcohol). Dry bonded is on the roadmap. |
Keeping duty-suspended and duty-paid stock apart
The core test of bonded software is whether you can say, for any pallet on the floor, whether duty has been paid on it. HMRC’s customs warehouse guidance is direct on this point. You must be able to identify the status of goods at all times, and you cannot use goods of different statuses to complete an order. Stock of different statuses can share a warehouse, but it cannot be mixed up in a pick.
In practice, that means status has to be captured at the door, not reconstructed later from paperwork. Clarus’s bonded stock logic tracks status from receipt to dispatch, so the status of a lot is visible from the goods-in scan through to the despatch. The warehouse manager confirms bonded status and tax type with scanner prompts as goods arrive, which is the cheapest point to catch a mistake. Lot-level control sits alongside this, and Clarus’s batch and lot control supports full recall readiness.
Records HMRC will expect
Keep records that show what you received, where it sits, its duty status, who owns it and what has left. For excise warehouses, HMRC expects records of all goods received, stored and removed, and the information must be permanent and legible. Anyone applying to run an excise warehouse has to show they can keep the commercial records set out in Excise Notice 206, and HMRC’s guidance on keeping records for an excise warehouse explains what must be shown.
The two regimes ask for different detail, as the table shows. Both expect records that HMRC can check later.
| Record | Excise warehouse | Customs warehouse |
|---|---|---|
| Stock position | Records of all excise goods received, stored and removed | Stock records showing current stock under the procedure, kept in real time |
| Duty status | Duty status of each good, with evidence of any duty paid | Status of goods identifiable at all times |
| Ownership | Owner’s name, address and VAT number where appropriate | Import declaration details supplied for goods put in by another party |
| Removals | Each removal recorded individually, with a schedule by type of removal | Temporary removals recorded, with HMRC permission obtained first |
| Operasjoner | Accounts taken immediately before and after each operation, with gains and losses reported | Duty management system records updated before midnight on the next warehouse operation day, where one is used |
For excise goods, movements also run through HMRC’s electronic system, and Excise Notice 197 sets out how goods are received into and removed from an excise warehouse. Clarus stamps each movement with the user, device, quantity, location and status decision, which covers the audit trail side. Its weekly HMRC-ready outputs itemise payable duty by product and tax type. The part the software cannot supply is the scan itself. A timestamp on a wrong scan is still a wrong record.
Movements in and out of bond
Every movement is a point where status can go wrong, so bonded software has to govern transfers, removals and dispatch as well as receipt. Under Excise Notice 197, excise goods are treated as warehoused once they enter the area HMRC has approved, which makes receipt a point of legal significance rather than an admin step.
Transfers inside the site need the same care as receipts. A transfer that moves a pallet to a new location should keep its duty status with it. If the record shows only the new location, you know where the stock is but not whether it can still be released as it stands. Test this with a real transfer during your trial, rather than assuming the status follows the pallet.
For each lot, the system should show how much stock sits in bond and how much becomes payable when it leaves. Clarus’s bonded feature describes showing what is held in bond, what is duty-paid and what is about to crystallise, so finance and dispatch work from the same figures. Duty stays deferred until goods leave bond, which is why the movement record matters as much as the stock count.
Customs warehousing and the paperwork behind it
Customs warehouses bring a different set of data. Mathew Buttar, a Clarus implementation consultant, says the system can hold each warehouse customer’s EORI number and send it through carrier or API integrations, or print it on a commercial invoice or dispatch note. He also names the product description, value, country of origin and place of manufacture as the details customers ask for when goods are declared.
Check the fields you need with your customs adviser before you rely on them, because the data depends on your declarations. HMRC’s guidance also expects a customs warehouse to be approved for the type of goods it accepts, including chilled, frozen and chemical goods, so the software cannot make that decision for you.
Where bonded software stops
Software records the warehouse, but it does not control everything that happens to stock. A WMS can show that a pallet left bond on a given date. It cannot control what happens once a load leaves the back door, or whether the right load goes on the right lorry. Plan the physical checks as carefully as the data entry.
Plan for errors in the gaps between steps. A pallet booked in as duty-paid by mistake, a removal recorded against the wrong lot, or a physical count that never reconciles to the system are the kind of problems that surface at audit time if nobody looks for them earlier. A short daily check that compares the system position with the floor turns a gap into a fix within a day, rather than a finding at the next HMRC visit.
Be clear about today’s limits as well. The Clarus bonded feature describes wet bonded alcohol, and dry bonded stock is on the roadmap. Direct filing with HMRC is also on the roadmap, so at present you export the outputs and submit them yourself. The feature page does not describe customs warehousing for other goods, so ask for a demonstration of your specific flows before you commit.
Many bonded sites also run as part of a wider 3PL-drift, with several clients sharing racking and staff. For a worked example of a bonded operation’s experience, read the Bartrums customer story. For the wider field of options, our det beste WMS-systemet for 3PL-leverandører guide covers it, and for budgeting questions see WMS-kostnad.
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