We build Shopify automation for DTC and B2B merchants past $1M in GMV who have outgrown one-app-per-problem and need the storefront properly wired into their fulfilment, finance, marketing, and CS stack. The interesting work isn’t a Shopify Flow - it’s the order-to-fulfilment chain, the inventory truth across channels, and the customer 360 that has to stay consistent whether the order came from the website, a wholesale portal, an Amazon channel, or a retail POS.
If you need a Shopify Plus agency to redesign your theme, we’re not the right call. If you have a working storefront and the backlog is full of integration and automation work that crosses system boundaries, that’s exactly what we do.
What we automate with Shopify
Each pattern below ships in production with monitoring, not as a one-off app install.
- Order-to-fulfilment automation. Order placed → fraud check → fulfilment routed to the right 3PL or warehouse based on SKU, geo, and inventory location → shipping label generated → tracking written back to the customer record → status synced to your CRM. The chain runs whether the order came from Shopify, Amazon, or wholesale.
- Inventory truth across channels. Real inventory levels reconciled across the website, marketplaces (Amazon, eBay, Walmart, Faire), retail POS, and the warehouse. Buffer logic per channel so you don’t oversell. Low-stock alerts to the right buyer.
- Customer 360 that survives across orders. Customer record stitched together across guest checkouts, returning customers, and B2B accounts. Lifetime value, RFM segments, returns history, and CS interactions written to the Customer object - or to a custom object in Shopify Plus B2B if that’s the right model.
- Refunds, returns, and exchanges automation. Return request → eligibility check (RMA rules per SKU, return window, condition) → label generated → restock or write-off decision → refund or store credit → accounting entry. Powered by Shopify Returns or by a third-party RMA app with Shopify properly wired in.
- Subscription and recurring-order automation. Subscription state changes (paused, skipped, swapped, churned) into your CRM and CS tool, dunning flows on failed payments, win-back automation on cancelled subscriptions. Tightly integrated with Recharge, Bold, or Shopify Subscriptions depending on your stack.
- B2B and wholesale workflows. Customer-specific catalogues and price lists, NET terms order approval, draft-order flows from a sales rep, and tax-exempt order handling. Shopify Plus B2B has improved fast - we lean on it where it fits and bring in a wholesale-specific app where it doesn’t.
- Shopify Flow for the everyday cases. Tag-based segmentation, fraud risk flagging, internal Slack notifications on high-value orders, draft order routing. Flow is great for in-Shopify logic - we use it where it fits and graduate to external orchestration when it doesn’t.
- Shopify Functions for storefront logic. Custom discount logic, shipping rate overrides, payment method customisations, and cart validation rules that the standard Discounts/Shipping app can’t express. Built in Rust or JS, deployed as a Shopify Function. Read our how to automate ecommerce post for the full pattern.
How we work with Shopify
Three layers, and we name which layer each problem sits in.
Layer 1: native Shopify. Shopify Flow for declarative in-store logic. Shopify Functions for cart/discount/shipping/payment logic. Theme app extensions for in-storefront UX. Native apps from the Shopify App Store when they cover the use case at a price worth paying. Everything documented and version-controlled where possible.
Layer 2: cross-system orchestration via Admin GraphQL and webhooks. When the workflow crosses Shopify and one or more external systems, the orchestration sits in n8n, Make, or custom code. Shopify’s Admin GraphQL API is the right surface for most operations, with REST as the fallback for the few endpoints that haven’t migrated. Webhooks are the right inbound trigger for order/customer/product/inventory events. We rate-limit-aware everything and use bulk operations for backfills. See our n8n automation guide for the patterns.
Layer 3: custom apps. When the workflow needs an embedded app surface (a custom admin page for ops users, a custom merchant tool, a private-app integration), we build a Shopify app proper - App Bridge, Polaris UI, OAuth, scoped down permissions, deployed to a managed runtime. Public app for the App Store is its own scoping conversation.
Discovery is one to two weeks of mapping the storefront, the order flow, the inventory truth, and the integration backlog. We scope per system and ship in priority order.
Common integrations
Where Shopify meets the rest of your stack:
- Klaviyo - purchase events to drive segmentation and flows, customer attributes back to Shopify for storefront personalisation. Walkthrough: Shopify and Klaviyo integration.
- QuickBooks, Xero, NetSuite - order-to-invoice sync, refund handling, payout reconciliation, and inventory cost flow. Sibling: QuickBooks automation.
- HubSpot, Salesforce - customer records to the CRM, post-purchase nurtures, B2B account sync. Siblings: HubSpot, Salesforce.
- Slack - high-value order alerts, low-stock notifications, RMA escalations. Sibling: Slack automation.
- ShipStation, Shippo, ShipBob, your 3PL - fulfilment routing, tracking sync, label generation.
- Gorgias, Zendesk, Front, Intercom - order context in the support inbox, refund and exchange flows from the help desk.
- Returnly, Loop Returns, Aftership - return request to refund/exchange chain.
- Amazon, eBay, Walmart, Faire - channel inventory and order sync.
- Recharge, Bold, Shopify Subscriptions - subscription state into CRM and CS.
- Your data warehouse (BigQuery, Snowflake, Redshift) - daily exports for analytics that the Shopify reports won’t give you.
What makes a 2V engagement different from a Shopify Plus agency
Most Shopify Plus agencies are design-and-build shops focused on theme, conversion, and front-end app integration. We’re operations engineers who work behind the storefront. Practical differences:
- We’re operations-first, not storefront-first. Each engagement names operational outcomes - orders fulfilled faster, inventory truth across channels, refund cycle time - not pixels.
- We own the automations end-to-end after delivery. Most Plus agencies hand you a build and bill for change requests. We keep the automations we shipped working. See our operations automation and marketing workflow automation pillars.
- We don’t push you off Shopify. If you’re on Shopify, we make it work. We don’t take referral fees from app vendors. App recommendations are based on what fits.
- We don’t theme. Theme work is a different discipline. If you need theme + automation, we’ll partner with your theme agency rather than try to do both.
- We’re cross-stack. When the workflow leaves Shopify - into your 3PL, your warehouse, your finance system - that’s the same engagement.
When to hire us vs hire in-house
Hire a full-time ecommerce ops manager or engineer when you have predictable, repeated work - daily inventory reconciliation, ongoing app maintenance, theme updates, dozens of Shopify Flows - and at least 30 hours a week of it. Most $1M-$20M merchants have the volume.
Hire us when:
- The integration backlog is full of items that cross Shopify and other systems your in-house team can’t all own.
- You need a Shopify Function, a custom embedded app, or a serious Admin GraphQL build and don’t want a developer on payroll.
- Your inventory truth across channels has been broken for months and nobody can fix it.
- You’re moving to Shopify Plus B2B and the migration touches your CRM and ERP.
- You’re past $1M in GMV and the automation gap is costing more than the engagement.
Pricing & engagement
We have a $5k project minimum. A typical single-system install - say, the order-to-fulfilment chain wired across Shopify, your 3PL, your CRM, and your finance system - runs $15-50k depending on the number of systems and channels in scope. Retainers for ongoing operation start at $1k/mo.
We don’t quote off a phone call. The Efficiency Scorecard gets us to a real number - 10 minutes of inputs and you’ll see where the highest-ROI Shopify work lives. The ROI calculator gives a rougher pre-engagement estimate.
FAQ
Do you work with Shopify Plus or also non-Plus stores?
Both. Plus unlocks Functions, B2B, Flow with custom-coded actions, dedicated launch engineer support, and higher API limits. Non-Plus stores can absolutely get serious automation; Plus just makes some patterns cheaper to build. We’ll flag during scoping if a particular project really wants Plus.
Can you work with our existing apps and theme?
Yes - that’s the default. We don’t rip out apps that are working. We integrate around them. If we recommend swapping an app, it’s because it’s actively costing more than it earns or blocking a key workflow.
How long does a typical Shopify automation project take?
The first system goes live in 4-6 weeks. A full backbone - order routing, inventory truth, customer 360, returns automation, finance sync - takes 4-8 months installed in priority order.
Do you build Shopify apps for the App Store?
We can, with a longer timeline. App Store review (security, performance, UX) adds 6-12 weeks. Most engagements end up with private apps used by your team or by a small set of merchants in your network, which skips that.
What about international, multi-currency, multi-region setups?
Yes. Shopify Markets is solid for most international setups; we wire pricing rules, tax handling, and shipping logic per market. For Markets Pro or a custom international model, we scope the tax and compliance flow carefully - that’s an area where shortcuts come back to bite you.
Do you handle headless Shopify or Hydrogen?
Lightly. The backend automation work (fulfilment, inventory, customer data, finance sync) is identical whether you’re using a Liquid theme or Hydrogen. The headless front-end build is a different discipline - we’ll partner with a headless agency for that side and own the backend.
What about Amazon, eBay, and other channels?
Yes. Multi-channel inventory and order sync is one of the most common requests. We use a channel platform (e.g., Tradevine, Linnworks, Cin7) when it fits and build custom against the marketplace APIs when it doesn’t.
Will the automations break on a Shopify update?
Shopify ships changes constantly. The Admin GraphQL API has a versioned release pattern that gives 12 months of notice. REST endpoints get deprecated more aggressively. Retainer clients get a monthly review against Shopify changelog; project-only clients get a handoff document flagging the parts most likely to need attention.
If Shopify is the storefront your business runs on but the automation behind it keeps coming up short, the Efficiency Scorecard is the right next step. Ten minutes in, you’ll see where the highest-leverage Shopify work lives. If your stack also leans on QuickBooks, HubSpot, or Slack, the scorecard maps those too.