The Top 5 Challenges of Multichannel Ecommerce and How to Solve Them
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Selling across multiple channels will give your ecommerce business more opportunities to grow and reach new customers.
For many businesses, multichannel selling is already becoming the norm. According to DHL’s 2025 Ecommerce Trends Report, 63% of global ecommerce businesses sell on at least three online platforms.
But with each additional channel, you add another set of orders, inventory, fulfillment workflows, and marketplace requirements to manage. Processes that worked just fine when you were selling on one or two channels can quickly become difficult to keep up with as your operation grows.
These problems can show up as more manual work, employees jumping between different platforms, inventory discrepancies, complicated fulfillment, and difficulty keeping up with each marketplace’s requirements.
The key is having the right systems in place before these problems start slowing your business down. A multichannel operating system can help you overcome the operational challenges of selling across multiple channels. In this post, we’ll look at five of the most common challenges of multichannel selling and how a multichannel operating system can help you overcome them.
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1. Time-Consuming Manual Processes
The Challenge
Many ecommerce businesses start managing their inventory with manual processes because they are inexpensive and relatively easy to manage at low order volumes. If this is you, you’re probably downloading, printing, and entering orders manually, updating inventory in spreadsheets, and entering tracking information into multiple systems.
These tasks don’t necessarily cause problems when you’re processing a manageable number of orders, but this strategy doesn’t work long-term.
As order volume and channel count increase, every manual task creates another opportunity for delays and errors. You might try to hire more people to keep up with the repetitive work, but this can increase your operating costs without actually fixing the underlying problem.
How a Multichannel Operating System Helps With Manual Processes
A multichannel operating system (MCOS) is a software platform that brings your inventory, orders, product listings, and fulfillment across multiple channels all together into one centralized dashboard. It helps by consolidating your scattered workflows so that you have one source of truth, from listing creation to final delivery.
Most multichannel operating systems will have automation features, which will help you solve the issue of time-consuming, tedious manual processes. You’ll be able to automate repetitive workflows, such as importing orders, updating inventory, generating fulfillment information, and syncing tracking data.
Once you set up the rules that your business runs on, you won’t have to intervene manually with every order. The system can handle routine decisions automatically, leaving your team to focus on exceptions and higher-value operational work.
2. Managing Multiple Ecommerce Channels and Platforms
The Challenge
Another issue is just how fragmented your operations can become when they are spread across multiple platforms.
This often happens as a business scales. Each marketplace or sales channel you expand to has its own dashboard, order data, inventory information, and requirements.
A simple question like, “Where is this order?” means your fulfillment team needs to jump between multiple systems, including Amazon, Walmart, Shopify, shipping platforms, warehouse systems, and spreadsheets. The bigger your operation gets, the harder it becomes for everyone to work from the same information.
How a Multichannel Operating System Centralizes Operations
A multichannel operating system can solve this problem by centralizing orders, inventory, fulfillment, and other operational data in one place. Instead of jumping between different platforms, your team has a single place to find the information they need.
The key is to connect all of your sales channels with your fulfillment and warehouse workflows, so you eliminate the need to move information between systems.
3. Keeping Inventory Synchronized Across Channels
The Challenge
How often do your inventory levels get updated across each platform?
A delay or a discrepancy in your inventory can lead to overselling, which can do serious damage to your brand. A disappointed customer who didn’t get the product they ordered may leave a bad review, impacting your future sales and negatively affecting your brand image. Plus, canceled orders, delayed fulfillment, and customer complaints can cause you to incur marketplace penalties and can bring down your seller metrics.
This problem becomes even more complicated when your inventory is spread across multiple warehouses, 3PLs, FBA/WFS, or other fulfillment methods. (For a deeper dive into this issue, take a look at our blog post How to Stop Overselling Across Amazon, Walmart, and Shopify.)
How a Multichannel Operating System Improves Inventory Management
To solve this issue, every sales channel you operate on needs an accurate picture of available inventory. So, if a customer buys the last unit on Amazon, the inventory needs to be instantly updated across Walmart, Shopify, and all of your other channels.
When you synchronize your inventory across all connected sales channels, you’ll have a centralized view of all available stock, and inventory will be updated as orders come in. You can even incorporate inventory buffers to provide additional protection against overselling. If you have multiple fulfillment locations, you’ll have visibility into your inventory by warehouse and location.
4. Multichannel Order Fulfillment and Shipping
The Challenge
Every time an order comes in, a decision needs to be made about where and how it should be fulfilled. When you only have one warehouse, this is relatively straightforward. But when you start to have multiple warehouses, 3PLs, FBA/WFS, or other fulfillment methods, deciding where an order should go becomes much more complicated.
If you route an order to the wrong fulfillment location, this can mean higher shipping costs, longer delivery times, and unnecessary transfers - and can increase the need for manual intervention. As order volume increases, manually making these decisions becomes increasingly difficult because different channels also have different shipping requirements and SLAs.
How a Multichannel Operating System Simplifies Order Fulfillment
Automated order routing takes much of the decision-making out of fulfillment. When an order comes in, the system will automatically consider factors such as inventory availability, warehouse locations, customer location, shipping costs, and product requirements.
It will send the order to the appropriate fulfillment location, without anyone needing to make the decision manually. This will help your team to meet delivery expectations efficiently while still controlling fulfillment costs.
5. Keeping Up With Marketplace Requirements and Performance
The Challenge
Another major challenge that ecommerce sellers face is managing requirements around fulfillment, shipping, cancellations, tracking, and customer experience. It’s crucial to meet these requirements across every channel you operate on, but it’s not always easy to do so (and it gets more challenging the more channels you have!)
When information is fragmented, it becomes harder to identify problems before they can affect marketplace performance. Plus, a process that works for one channel won’t necessarily satisfy another channel’s requirements. Missing shipping deadlines, inaccurate tracking, order cancellations, and other issues will affect your seller metrics and damage your account health.
For example, a delay in updating tracking information might be a minor administrative issue internally, but it can become a marketplace performance issue if the channel expects tracking information within a specific timeframe.
How a Multichannel Operating System Helps Manage Marketplace Requirements
A multichannel operating system can help you keep track of marketplace requirements by bringing together orders, fulfillment, and tracking information to give your team visibility across channels. Instead of checking each marketplace separately, your team can manage these workflows from a centralized dashboard.
Automation can also help you stay on top of channel-specific requirements. You can set up rules for order routing, fulfillment, and shipping so that orders are processed according to the requirements of each channel. Tracking information can then be synced back to the appropriate marketplace automatically, reducing the risk of missed updates or inaccurate information.
Having all of this information in one place also makes it easier to identify issues before they become bigger problems. You can see where orders are in the fulfillment process, monitor exceptions, and quickly address anything that could affect your marketplace performance.
The Key to Managing Multichannel Ecommerce Operations
As your business adds sales channels, the operational side of multichannel selling becomes harder to manage manually.
The right systems can help you handle that complexity without relying on more spreadsheets, manual data entry or people constantly switching between platforms. A multichannel operating system brings your sales channels, inventory, and fulfillment workflows together, while automation takes care of many of the repetitive decisions happening behind the scenes.
If your current processes are becoming harder to manage as you add channels, it may be time to look at how much of that work can be centralized and automated. You can try a demo of Goflow to see how a multichannel operating system can help you manage orders, inventory, and fulfillment from one place.