Understanding B2B Workflow Automation for Ecommerce in 2025

If fulfilling a B2B order requires five emails, four spreadsheets, and a gentle nudge for accounting, it’s time to switch gears.  

When you shift from B2C to B2B, simple pricing, instant payments, and one-click shipping are replaced with bulk orders, negotiated pricing, tax exemptions, and channel-specific rules, making the entire journey complex for both sellers and buyers.

As one Amazon seller put it, 

“I get one deposit every two weeks from Amazon, and that one deposit can have 1000+ sales receipts tied to it. I literally start to go cross-eyed after a while!”

That’s just one example of how quickly things can spiral without automation, especially when selling B2B at scale. 

From order processing and inventory management to accounting and multi-channel reconciliation, we’ll break down the workflows that matter most and show you how to automate them using tools like Webgility.

So where do you start, and which B2B workflows are worth automating first? 

Key B2B workflows that get easier with automation

Before we dive into how each workflow can be improved, let’s understand what b2b workflow automation ecommerce really looks like in practice.

1. Order processing 

Typically, an order includes custom SKUs, negotiated prices, purchase orders, and specific delivery terms. 

Once the order comes in, sellers manually transfer that information into their ERP or accounting system and notify the warehouse via emails or spreadsheets. (a sure-shot way for errors and delays) .

How automation helps

Whether you get an order from Amazon, BigCommerce, or Shopify, an automation tool can import orders directly from the sales channel and sync them directly with their accounting software so that you can trigger warehouse actions in real time. 

Note: If you use Webgility, it can sync Purchase Order numbers (PO#s), match company customers, and map payment terms for Shopify Plus and BigCommerce to automate order management. 

2. Customer onboarding and approval 

Buyers often submit business credentials and tax-exemption certificates and need approvals for net payment terms. After verification, sellers assign them to the right pricing tiers or customer groups. When done manually, this leads to slow onboarding and inconsistent records. 

How automation helps

Automation can streamline this entire flow. You can auto-tag customers based on submitted credentials, sync tax exemption statuses directly to your accounting platform, and assign pricing tiers using pre-set rules to ensure each customer gets the right experience from day one.

3. Payment and invoice management 

Whether you sell on Shopify, Amazon, or BigCommerce, your sales don’t always match when the money lands in your account. Many B2B sellers also offer Net 30 or Net 60 terms, meaning payments are delayed even further. 

Managing this manually involves generating invoices outside the ecommerce system, tracking due dates in spreadsheets, and waiting weeks for payment. Then, you manually reconcile everything once the funds hit the account. For sellers working across multiple sales channels, this gets even more complicated. 

How automation helps

With tools like Webgility,  you no longer need to enter receipts to process P&L statements, as it scans invoices and automatically builds reports for them. Plus, bulk payments (like Amazon payouts) are matched against the individual sales receipts that make up the deposit. This saves hours of back-office work and improves accuracy.

4. Inventory, cancelling orders, and reordering 

You often have to adjust stock levels one platform at a time, manually update spreadsheets when orders are cancelled, and track reorder points based on gut feel or past emails. Even though platforms like Amazon and Shopify let you manage multiple stores under a single seller account, keeping each store’s inventory aligned without overlap can quickly become messy.

How automation helps 

Automation tools like Webgility improve inventory management as it syncs inventory in real time across all your channels. When an order is canceled or returned, stock levels are auto-adjusted. You can also set low-stock alerts and automate purchase orders based on historical demand to avoid stockouts or excess inventory. 

5. Shipping and fulfillment

Printing labels, updating tracking numbers by hand, and coordinating with third-party logistics (3PLs) gets tiring fast, especially when orders pour in from different sales channels with unique requirements. 

How automation helps 

With automation in place, orders are automatically routed to the correct fulfillment partner. Tracking numbers are pulled directly into your ecommerce system, and customer notifications are sent without you lifting a finger. 

Webgility ensures accurate SKU and order data flow between your storefront and fulfillment platforms, cutting down on manual errors and shaving hours off your shipping process.

6. Tax and compliance 

Depending on the buyer's location and exemption status, you may need to apply or waive sales tax. You may manually collect certificates and input data into your accounting systems. Not only is this time-consuming but also error-prone and hard to scale. 

How automation helps 

Automation tools take over by applying correct tax rules using integrated tax engines, storing and syncing exemption information, and ensuring compliance across all platforms. 

If you use Webgility, it connects your ecommerce and accounting systems so transactions are recorded accurately and tax rules are applied consistently for accurate tax filing. 

7. Multi-channel sales reconciliation

If you're selling on Amazon, Shopify, or BigCommerce, your payouts come as lump-sum deposits that represent hundreds (or thousands) of individual sales. Manually matching each of these to invoices, adjusting for shipping costs and transaction fees, and then syncing them with your books eats up hours every week.

How automation helps 

Tools like Webgility automate this entire process. Each deposit is broken down and mapped to the corresponding sales receipts and then synced with your accounting software. It even factors in platform fees and shipping charges, giving you a clean, reconciled view across all channels. 

Now that you’ve seen where automation can lighten the load, let’s take it one step further: How exactly do you implement these solutions in your business?

How to automate these workflows: Practical solutions 

From bulk order processing to multi-channel sales reconciliation, automation tools can do the heavy lifting for your business. 

1. Streamline bulk orders and pricing adjustments 

Platforms like Shopify Plus and BigCommerce simplify the front-end buying experience for B2B customers. They allow you to:

• Display customer-specific pricing and product catalogs
• Apply tiered or negotiated discounts automatically 
• Enables bulk ordering with CSV uploads or quick order forms 

But what happens after the orders are placed, especially for accounting and operations? 

Once an order is submitted, Webgility automates order creation and accounting in the accounting software. You get a single dashboard that consolidates orders across channels like Shopify and BigCommerce. 

The tool syncs every order (including customer info, PO numbers, and line items) to your accounting software, reducing manual entry and helping you avoid costly errors. It even supports rules to auto-route orders to specific warehouses or fulfillment partners.

2. Keep inventory synced across all sales channels 

Say a wholesale customer places a bulk order for 500 units through your BigCommerce store, and you’re still selling smaller quantities on Amazon and Shopify. Without real-time inventory sync, you risk overselling, disappointing customers, and having to issue refunds or back orders.

Webgility syncs your inventory levels in real time across your connected platforms and accounting systems. Here’s how it helps:

• Tracks inventory levels by sales channel
• Automatically matches existing products and catalogs or does bulk mapping of products
• Instantly updates inventory in QuickBooks for cancelled or refunded orders
• Forecast demand, make data-driven decisions on which inventory to purchase, and avoid overstocking with demand planning

As soon as you receive an order, inventory updates are updated everywhere so that the orders don't disrupt your inventory workflow.

3. Automate payment generation and reconciliation

B2B orders might include POs, Net 30 terms, partial payments, or negotiated invoices. Manually tracking these payment types delays accounting and leads to errors.

With an automation tool like Webgility, once an order is placed, the system can automatically post orders as sales receipts, invoices, or journal entries with complete details, including fees, taxes, shipping, discounts, and refunds.

No need for accounting teams to chase payment info or manually enter invoice data to get a clear financial picture.

4. Simplify shipping and order fulfillment

Shipping large B2B orders can involve multiple boxes, custom carriers, and freight options. 

With Webgility, orders are automatically routed to your shipping solution, and tracking info is synced back to your storefront so that customers are informed. 

It also connects with platforms like ShipStation and others to automatically pass on order details, shipping addresses, and packing info the moment an order is received. Moreover, it generates shipping labels, assigns tracking numbers, and marks orders as shipped across all your channels. 

5. Ensure tax compliance without manual effort 

The US alone has over 13,000 sales and use tax jurisdictions. Imagine how many tax laws and regulations you’d need to consider if you sell internationally!

When an order is placed, tools like Webgility automatically pull the tax data from your sales channel (whether that’s Shopify, Amazon, or BigCommerce), and map it correctly to your accounting software, like QuickBooks, NetSuite, or Xero.

If a customer is tax-exempt, it ensures that’s reflected in the invoice. If different states apply different tax rates, it records them properly so your filings stay accurate. 

For more complex needs, it integrates with Avalara for real-time tax rate validation and automated filing, resulting in fewer errors, faster processing, and audit-ready records. 

6. Automate manual multi-channel sales reconciliation

Say you receive a biweekly deposit from Amazon, which includes 800+ individual orders, each with its own product pricing, shipping charges, platform fees, and taxes. Meanwhile, your BigCommerce store generates high-volume bulk orders with custom pricing and Net 30 terms.

How does Webgility help you track what’s actually earned from both these sales channels? 

It pulls granular data from both BigCommerce and Amazon, breaks down every deposit, and matches it to the actual invoices, including fees, refunds, and taxes. Then, it generates accurate journal entries and syncs them to your accounting software.

Bonus read: A guide to manage multi channel ecommerce accounting 

The Bottom Line: Why B2B ecommerce brands trust Webgility

Most B2B ecommerce businesses hit a ceiling not because of demand but because the back end breaks as they grow. The more orders you win, the more tangled things get. 

Webgility understands these operational bottlenecks and simplifies operations by automating order syncing, inventory updates, payment reconciliation, and tax calculations. 

If you need additional tools for customer approvals, procurement management, or contract-based payments, pair Webgility with a CRM or ERP to create a fully streamlined workflow.

It also plugs into leading marketplaces, ecommerce platforms, POS systems, and accounting software, so you don’t have to worry about whether it’ll fit into your tech stack. Ready to simplify complex B2B workflows with Webgility? Get started for free today!