# Does Flexport handle customs and duties documentation for a Shopify Markets international order differently than a domestic-only 3PL would?

Reviewed by Martin Dejnicki, Director of SEO & AI Search · facts verified October 11, 2026 · canonical: https://deploi.ca/shopify/faq/flexport-customs-duties-docs-international-orders

## Short answer

Flexport handles customs paperwork on a Shopify Markets order no differently from a domestic-only third-party logistics (3PL) provider, because the merchant-of-record setup decides it. Under Managed Markets, Global-e handles "duties, tax remittance, commercial invoices, and carrier arrangements" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026). Flexport differs on imports: its own licensed broker clears your stock into the US ([flexport.com](https://www.flexport.com/terms-and-conditions/), October 2026).

- **Who handles Managed Markets paperwork:** Global-e, as merchant of record. Global-e handles duties, tax remittance, commercial invoices and carrier arrangements, and Managed Markets assigns Harmonized System (HS) codes to products automatically. ([Shopify Help Center, Overview of Managed Markets](https://help.shopify.com/en/manual/international/managed-markets/overview))
- **Fulfillment services Shopify lists:** Flexport, ShipBob, ShipStation and three more. Cymbio, Fulfil.io and ShipHero Inventory and Shipping complete the list for Managed Markets orders, and each needs an extra integration step to buy Managed Markets labels. ([Shopify Help Center, Fulfilling and managing Managed Markets orders](https://help.shopify.com/en/manual/international/managed-markets/fulfillment))
- **Managed Markets fee:** 3.5% per transaction, 3.25% on Plus. Add the store's own currency conversion fee: Shopify's pricing pages show 1.5%, while its Help Center lists 2% outside the US. ([Shopify Help Center, Overview of Managed Markets](https://help.shopify.com/en/manual/international/managed-markets/overview); [Shopify, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/international/pricing); [Shopify Help Center, Fees and costs](https://help.shopify.com/en/manual/international/pricing/fees); [Shopify Canada, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/ca/international/pricing); [Shopify UK, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/uk/international/pricing))
- **Flexport's US import broker:** Flexport Customs LLC. Flexport calls it "a licensed customs broker with a national permit". Its Shopify freight app uses it for China-to-US ocean freight and supports no third-party brokers. ([Flexport, Flexport Terms and Conditions](https://www.flexport.com/terms-and-conditions/); [Flexport Help Center, The Flexport App on Shopify](https://www.flexport.com/help/shopify-app/))

## Deploi's call

Fix the catalog, then choose the merchant-of-record model, then choose the third-party logistics (3PL) provider. Run in that order and the 3PL question stops being a customs question at all.

**BUY: Choose the warehouse on fulfillment, not customs, when**

- Your international orders are outbound parcels from a US warehouse, because your merchant-of-record setup, not the warehouse, sets their duties.
- You sell through Managed Markets, where Global-e prepares commercial invoices and Shopify lists Flexport, ShipBob and ShipStation alike ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/fulfillment), October 2026).
- You buy from US suppliers, so no import entry needs a broker.
- You run one US warehouse at roughly 500 to 10,000 orders a month, the band [the ShipBob vs. Flexport record](https://deploi.ca/shopify/build-vs-buy/shipbob-vs-flexport) scores BUY for ShipBob (October 2026).

**DEPENDS: Weigh Flexport's customs side when**

- You import containers and want the customs broker beside the warehouse, since Flexport's Shopify freight app supports no third-party brokers ([Flexport Help Center](https://www.flexport.com/help/shopify-app/), October 2026).
- Import classification errors cost you money, and Flexport's licensed brokers "confirm every code" ([Flexport](https://www.flexport.com/products/product-classification/), October 2026).
- You export goods you imported: Flexport's drawback page says "If you export, you may qualify for refunds" ([Flexport](https://www.flexport.com/products/duty-drawback/), October 2026).
- Inbound freight and fulfillment must sit with one vendor, the case [the record](https://deploi.ca/shopify/build-vs-buy/shipbob-vs-flexport) keeps for Flexport (October 2026).

## Which customs events does a Shopify Markets order involve?

A Shopify Markets order of imported goods involves two separate customs events, with different owners, documents and money. The first is the import: a container of your stock entering the United States. The second is the export: one parcel leaving your warehouse for an international customer. Advice goes wrong when both get called "customs", so keep them apart before you compare Flexport with a domestic-only third-party logistics (3PL) provider. [Whether Flexport adds anything for a US-domestic-only brand](https://deploi.ca/shopify/faq/flexport-vs-shipbob-us-domestic-shipping) covers the case with no border at all.

**Flexport's customs difference sits on the import; the export parcel's paperwork follows the merchant-of-record setup**

| Question | Import into the US | Export to your customer |
| --- | --- | --- |
| What crosses the border | A container of your inventory | One parcel from a Markets order |
| Who owns the paperwork | Your customs broker | The merchant of record: Global-e on Managed Markets, you otherwise |
| What Flexport does | Clears it through its own licensed broker, drayage included | Ships the parcel on the label your setup needs |
| What decides duty treatment | Classification and valuation at entry | Your Markets duty settings and merchant-of-record choice |
| What a domestic-only 3PL does | No brokerage; your broker clears the stock first | The same as Flexport |

Sources: [Shopify Help Center, Overview of Managed Markets](https://help.shopify.com/en/manual/international/managed-markets/overview); [Shopify Help Center, Fulfilling and managing Managed Markets orders](https://help.shopify.com/en/manual/international/managed-markets/fulfillment); [Flexport, Flexport Terms and Conditions](https://www.flexport.com/terms-and-conditions/); [Flexport Help Center, The Flexport App on Shopify](https://www.flexport.com/help/shopify-app/). Verified October 9, 2026.

## What changes on the outbound parcel if Flexport ships it?

Very little changes on the outbound parcel if Flexport ships it, because the paperwork follows your merchant-of-record setup, not the warehouse. On Managed Markets, Global-e "creates commercial invoices and remits them where they're needed" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026). Shopify lists six compatible fulfillment services for Managed Markets orders, Flexport, ShipBob and ShipStation among them. Each one needs "an additional integration step to purchase Managed Markets labels" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/fulfillment), October 2026).

When you stay merchant of record yourself, the warehouses offer the same menu. Flexport ships "to over 200 countries and territories" with delivered duty paid (DDP) and delivered duty unpaid (DDU) options ([Flexport](https://www.flexport.com/products/ecommerce-fulfillment/), October 2026). ShipBob's system "generates the necessary documentation automatically" for cross-border orders, though "ShipBob is not a customs broker" ([ShipBob](https://www.shipbob.com/ecommerce-fulfillment/international-fulfillment/), October 2026). So the outbound parcel doesn't separate Flexport from other warehouses.

## Who sets duties on a Markets order: the warehouse or the merchant of record?

The merchant of record sets duties on a Markets order, not the warehouse that picks it. Shopify says that with Shopify Markets on its own, "you remain the merchant of record, so tax registration, duties, and customs compliance stay your responsibility" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026). Shopify can collect duties at checkout for 0.5% per transaction, a temporary rate against a regular 0.85% with Shopify Payments ([Shopify](https://www.shopify.com/international/pricing), [Shopify Help Center](https://help.shopify.com/en/manual/international/duties-and-import-taxes/charging-duties), October 2026).

Managed Markets hands those responsibilities to Global-e as merchant of record, for 3.5% per transaction, or 3.25% on Plus, plus the store's currency conversion fee ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026). Either way, the warehouse that picks the parcel sets none of the duty treatment, so brief Flexport or any other warehouse only after you choose. [Whether Managed Markets pays its way under $5M of international sales](https://deploi.ca/shopify/faq/managed-markets-worth-it-under-5m-international-sales) runs the cost case.

## How should a brand set up international duties, in order?

A brand should set up international duties in five steps, in this order, so the warehouse is briefed last:

1. **Fix the catalog first.** Give every product a Harmonized System (HS) code and a country of origin, because Shopify calculates self-managed duties from both ([Shopify Help Center](https://help.shopify.com/en/manual/international/duties-and-import-taxes/charging-duties), October 2026). Managed Markets assigns its own codes, which "might differ from the ones that you initially entered" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026).
1. **Choose the merchant-of-record model.** Stay your own merchant of record on Shopify Markets, or hand the role to Global-e through Managed Markets. [Who can use Managed Markets](https://deploi.ca/shopify/faq/managed-markets-plus-only-or-advanced-plan) is its own answer.
1. **Choose duty-paid or duty-unpaid per market.** Managed Markets stopped supporting delivered duty unpaid (DDU) on 24 August 2026 wherever it supports delivered duty paid (DDP) ([Shopify Changelog](https://changelog.shopify.com/posts/managed-markets-is-ending-delivered-duty-unpaid-ddu-support), October 2026). A small number of destinations still ship DDU, because Managed Markets "can't calculate duties and import taxes for them" ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/overview), October 2026).
1. **Then brief the warehouse.** If you collect duties yourself, the warehouse must buy DDP labels, or "your customer pays for the duties and import taxes twice" ([Shopify Help Center](https://help.shopify.com/en/manual/international/duties-and-import-taxes/additional-tasks), October 2026).
1. **Keep the import separate.** If you import from China, judge Flexport's brokerage on that lane as its own decision, on classification accuracy and detention costs.

## When does Flexport's customs side help?

Flexport's customs side helps when the import is the problem, not the outbound parcel:

- **When import classification is costing you.** Flexport's licensed brokers "confirm every code" ([Flexport](https://www.flexport.com/products/product-classification/), October 2026), and a broker beside the warehouse shortens the loop between an error and the person who can fix it.
- **When you export goods you imported.** Flexport's drawback page says "If you export, you may qualify for refunds" ([Flexport](https://www.flexport.com/products/duty-drawback/), October 2026). ShipBob answers the same cost with Foreign-Trade Zone (FTZ) warehouses that "defer or eliminate duties on qualifying inventory" ([ShipBob](https://www.shipbob.com/ecommerce-fulfillment/international-fulfillment/), October 2026).
- **When you want stock in Canada or the UK.** Flexport launched fulfillment there on 2 September 2026 and says it "can clear customs directly" ([Flexport](https://www.flexport.com/blog/flexport-launches-fulfillment-services-in-canada-and-the-united-kingdom/), September 2026). For a US store, Managed Markets ships only from fulfillment locations in the continental US ([Shopify Help Center](https://help.shopify.com/en/manual/international/managed-markets/shipping/requirements-and-considerations), October 2026), so plan those markets outside it. [What customers notice with a warehouse abroad](https://deploi.ca/shopify/faq/managed-markets-vs-diy-3pl-delivery-experience) covers that trade.

## When doesn't Flexport's customs side help?

Flexport's customs side doesn't help when there's no import for it to clear, or when you won't hand that import to Flexport's broker. In these cases a domestic-only warehouse does the same job:

> **When not to do this**
> - **When your international volume is outbound parcels only.** Any competent warehouse ships those, and your Markets setup decides the duty treatment.
> - **When you buy from US suppliers.** There's no import entry to broker.
> - **When you'd keep your own customs broker.** Flexport's Shopify freight app supports Flexport's brokerage only ([Flexport Help Center](https://www.flexport.com/help/shopify-app/), October 2026), and its App Store listing reads "not currently available" ([Flexport on the Shopify App Store](https://apps.shopify.com/flexport), October 2026).

*These are operational and platform mechanics, not customs, tax or trade-compliance advice for your jurisdiction; classification decisions belong with a licensed customs broker.*

## Deploi's point of view

**Where we disagree.** Vendor material blurs inbound brokerage and outbound parcel documentation into one "customs handled" claim, and buyers read it as a differentiator on their Markets orders. It is not. It is a differentiator on the container, and the container is a different project with a different sponsor.

**What this page adds.** The parent asks whether Flexport adds anything for a US-domestic-only brand. This page takes the international case: import entries and outbound parcels are separate customs events with separate owners, the merchant-of-record setup rather than the warehouse sets duties on a Markets order, and Shopify lists Flexport beside ShipBob and ShipStation for Managed Markets fulfillment.

## When this answer changes

- Shopify changes the Managed Markets fee: 3.5% per transaction, or 3.25% on Plus, as of October 2026.
- Shopify settles its currency conversion rate outside the US: its pricing pages show 1.5%, while its Help Center lists 2% (October 2026).
- Shopify adds or drops fulfillment services on its Managed Markets compatibility list, or changes who prepares commercial invoices.
- Managed Markets ends delivered duty unpaid (DDU) shipping in the destinations that still use it.
- Flexport's Shopify freight app accepts third-party customs brokers, or Flexport opens fulfillment in more countries.

## Sources

1. [Shopify Help Center, Overview of Managed Markets](https://help.shopify.com/en/manual/international/managed-markets/overview), checked October 9, 2026
2. [Shopify Help Center, Fulfilling and managing Managed Markets orders](https://help.shopify.com/en/manual/international/managed-markets/fulfillment), checked October 9, 2026
3. [Flexport, Flexport Terms and Conditions](https://www.flexport.com/terms-and-conditions/), checked October 9, 2026
4. [Flexport Help Center, The Flexport App on Shopify](https://www.flexport.com/help/shopify-app/), checked October 9, 2026
5. [Shopify, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/international/pricing), checked October 9, 2026
6. [Shopify Help Center, Fees and costs](https://help.shopify.com/en/manual/international/pricing/fees), checked October 9, 2026
7. [Flexport, eCommerce Order Fulfillment Services](https://www.flexport.com/products/ecommerce-fulfillment/), checked October 9, 2026
8. [ShipBob, International Fulfillment: Global Ecommerce Fulfillment Services](https://www.shipbob.com/ecommerce-fulfillment/international-fulfillment/), checked October 9, 2026
9. [Flexport, HS Code Classification & Duty Minimization](https://www.flexport.com/products/product-classification/), checked October 9, 2026
10. [Flexport, Refunds on Import-Export Duties](https://www.flexport.com/products/duty-drawback/), checked October 9, 2026
11. [Shopify Help Center, Collecting international duties and import taxes at checkout](https://help.shopify.com/en/manual/international/duties-and-import-taxes/charging-duties), checked October 9, 2026
12. [Shopify Canada, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/ca/international/pricing), checked October 9, 2026
13. [Shopify UK, Pricing for Shopify's international sales tools and Shopify Managed Markets](https://www.shopify.com/uk/international/pricing), checked October 9, 2026
14. [Shopify Changelog, Managed Markets is ending Delivered Duty Unpaid (DDU) support](https://changelog.shopify.com/posts/managed-markets-is-ending-delivered-duty-unpaid-ddu-support), checked October 9, 2026
15. [Shopify Help Center, Additional tasks for collecting duties and import taxes at checkout](https://help.shopify.com/en/manual/international/duties-and-import-taxes/additional-tasks), checked October 9, 2026
16. [Flexport, Flexport Launches Fulfillment Services in Canada and the United Kingdom](https://www.flexport.com/blog/flexport-launches-fulfillment-services-in-canada-and-the-united-kingdom/), checked October 9, 2026
17. [Shopify Help Center, Requirements and considerations for shipping with Managed Markets](https://help.shopify.com/en/manual/international/managed-markets/shipping/requirements-and-considerations), checked October 9, 2026
18. [Flexport, Flexport Freight Made Easy on the Shopify App Store](https://apps.shopify.com/flexport), checked October 11, 2026
19. [Deploi Build vs. Buy, ShipBob vs. Flexport on Shopify: Which 3PL Wins?](https://deploi.ca/shopify/build-vs-buy/shipbob-vs-flexport), checked October 9, 2026, Deploi research