Be honest. What’s evolved faster – ecommerce as an industry, or your internal operations?
Shopify stores grow, diversify and scale, but so do the complexities that come with running them. Inventory moves unpredictably. Customers expect instant fulfilment updates. Data needs cleaning before it’s useful. And even merchants who already use basic automations often find themselves plateauing: the simple stuff is taken care of? Sure. But those deeper inefficiencies are still outstaying their welcome...
What’s changing now is how Shopify merchants view automation itself. It’s no longer a convenience or a way to save an hour a day. It’s becoming the foundation that rewrites core operational pain points. In a landscape shaped by rising customer expectations and volatile supply chains, Shopify automation is essential infrastructure.
This article explores five instances of hidden friction inside most ecommerce operations today – and how more nuanced and strategic automations can shine a light and fix the problem.
Why Today’s Operational Pain Points Need Stronger Automation
Ecommerce teams used to work in predictable cycles: order comes in, stock gets adjusted, fulfilment dispatches, marketing follows up. Today, the rhythm is often less linear. Inventory changes hourly. Customer behaviour shifts in days. Small inefficiencies compound quickly.
Manual processes have a few inherent issues:
- They rely on perfect human timing.
- They risk breaking under pressure or scale.
- They create inconsistent customer experiences.
- They hide the true operational cost of administration.
Advanced ecommerce workflow automation can help to solve these issues – not by replacing human judgement, but by handling the repetitive, time-sensitive or precision-based tasks that humans simply aren’t designed to manage at scale.
In this article we’ll take a look at five ecommerce pain points – common issues that negatively impact your online store – and show the automations that merchants are already leveraging to sidestep the problem and move ahead.
Pain Point #1 Fulfilment Delays Caused by Multi-Location Orders
The hidden problem
As Shopify stores grow, fulfilment networks grow with them. Many merchants operate across multiple warehouses, retail stores or 3PLs. The complexity surfaces when an order needs to be split (or partially sourced) from more than one location.
If a fulfilment team doesn’t realise an order spans multiple facilities, delays can emerge instantly: misrouted stock, duplicated picking, longer dispatch times and frustrated customers.
The risk it that these issues don’t show up in dashboards – they happen quietly, order by order.
Automation that solves it
Workflow: Get Notified When an Order Involves Multiple Fulfilment Locations
This workflow automatically checks every new order for multiple fulfilment locations. When detected, it immediately alerts the team with a breakdown of which locations are involved.
The benefit: no fulfilment surprises. Teams can coordinate early, avoid mis-picks and speed up dispatch. This is especially critical for high-volume stores or those using (or planning to use) hybrid fulfilment models.
Pain Point #2 Margin Erosion from Products Priced Below Cost
The hidden problem
Pricing errors happen more often than most merchants realise – particularly in stores with large catalogues, frequent updates or multiple contributors.
A single product priced below cost might go unnoticed for days or weeks. Multiply that across variants, collections, or sales events and the revenue impact becomes significant. But what if manual price checks aren’t realistic at scale or under increased pressure?
Automation that solves it
Workflow: Receive Daily Email Alerts for Product Price Below Cost
Triggered whenever a product is created or updated, this workflow evaluates all variants to detect price-below-cost discrepancies. If an issue exists, it sends a detailed email alert to the store admin – but only once per day per product, preventing notification overload.
The benefit: instant visibility into those silent margin-killers. Merchants avoid accidental loss-making listings and maintain healthy pricing hygiene across large or frequently changing catalogues.
Pain Point #3 Delayed Fulfilment When Orders Aren’t Routed to the Right Distributor
The hidden problem
For many merchants, and especially those in wholesale, distribution-heavy or multi-region operations, orders need to be sent to different distributors, based on where they’re going.
But routing orders manually by shipping zone can be error-prone. Missed routing means late deliveries, frustrated distributors and inefficiency that compounds as order volume grows.
Automation that solves it
Workflow: Email the Right Distributor for Orders in Specific Shipping Zones
Triggered when an order is paid, this workflow instantly checks the order’s shipping zone. If it matches a designated region, it automatically sends the correct distributor an email with order details and shipping information.
The benefit: distributors get what they need when they need it, without operational drag. Orders move faster, fulfilment partners stay aligned and the merchant avoids all the manual routing overhead – preserving their relationship with customers and distributors alike.
Pain Point #4 Lost Revenue When Authorized Payments Expire Uncaptured
The hidden problem
Shopify authorizes a customer’s payment but doesn’t always capture it automatically – especially in stores that manually review orders, accept B2B payments or operate in higher-risk verticals.
If the team misses the authorization window (typically 7 days), the payment expires. Expired authorizations = lost revenue and frustrated customers. As order volume grows, manual monitoring becomes unmanageable.
Automation that solves it
Workflow: Automatically Capture Payment Before Authorization Expires
Triggered for orders in a pending financial status, this workflow monitors each payment. If the payment remains authorized after 7 days, it automatically captures it and tags the order as AUTOCAPTURED for easy identification.
The benefit: a safety net for revenue protection. Merchants stop losing sales to expired authorizations and regain hours of manual financial admin time.
Pain Point #5 Errors and Compliance Risks from Invalid EU VAT Numbers
The hidden problem
For merchants selling into Europe (especially B2B) valid VAT numbers are essential. Incorrect or fraudulent VAT numbers create problems including:
- Incorrect tax handling
- Compliance issues
- Refunds or re-processing
- Delayed fulfilment while teams manually verify information
Manual VAT validation isn’t just slow – it’s unreliable.
Automation that solves it
Workflow: Validate a Customer’s EU VAT Number
Whenever a customer is created or updated, this workflow checks for a VAT number. If one is present, it automatically validates it via Abstract API to confirm accuracy.
The benefit: cleaner customer records, reduced tax errors, and smoother B2B onboarding – without needing human intervention. Fulfilment moves faster because VAT information is trusted from the moment it enters the system.
Automation as an Operational Strategy, Not a Tool
The merchants performing best today aren’t simply automating tasks – they’re designing their operations around automation. Whether it’s routing orders to the right distributor, validating VAT numbers before fulfilment or safeguarding revenue by capturing payments on time – these aren’t isolated conveniences, they’re systemic safeguards.
Each of the workflows highlighted above prevents a specific type of operational breakdown: expired authorizations, misrouted orders, pricing errors, compliance gaps. When combined, they form a resilience layer across the entire business. Instead of reacting to problems after they occur, merchants are building invisible guardrails that prevent issues from happening in the first place. At no extra burden to their teams.
This shift – from reactive fixes to proactive operational design – is where modern ecommerce gains its real edge. Automation as infrastructure: the connective layer that keeps pricing accurate, payments secure, distributors informed and tax data compliant.
Why Shopify Merchants Choose Arigato Automation
As stores scale, the risks and complexities multiply: more fulfilment locations, more cross-border customers, more pricing changes, more financial oversight.
Arigato gives merchants the depth and flexibility needed to solve these higher-order operational challenges. Its workflows allow teams to:
- Build multi-step logic
- Validate data against external APIs
- Monitor financial statuses over time
- Trigger notifications based on geographic rules
- Analyse product attributes at the variant level
It’s automation built for real-world operations – where timing, accuracy and conditional logic matter. And just as important, merchants get access to a support team that understands the intricacies of Shopify’s data model and can help translate business processes into automated workflows.
Ecommerce pain points aren’t going away – they’re evolving. The merchants who thrive in 2025 are the ones who treat automation not as a set of shortcuts, but as a strategic layer that protects revenue, ensures compliance, and keeps fulfilment running smoothly.
From capturing payments before they expire to validating VAT numbers, the most valuable automations are the ones that quietly eliminate the issues most teams only notice once it’s too late.
Ready to build a more resilient operation, explore what’s possible with workflows built for real Shopify complexity?