For mid-market multi-channel retailers, the revenue upside of selling across multiple platforms is undeniable. Consumers can find your products wherever they prefer to shop, and expanding your digital footprint is often the fastest path to growth. According to Digital Applied, retailers selling on three or more channels generate 143% more revenue per customer than single-channel sellers, with multi-channel customers converting 4.2 times the rate of single-channel shoppers.
But behind the scenes of a thriving multi-channel eCommerce operation, finance and operations teams are managing orders from each platform separately, attempting to reconcile inventory counts manually, tracking payment processor fees in elaborate spreadsheets, and assembling financial reporting from multiple disconnected dashboards. The chief financial officer’s (CFO) month-end closing becomes a tedious exercise in chasing data from Amazon, Shopify or Walmart, among others, before an accurate financial picture finally comes together.
These operational complexities can quickly erode those top-line gains, but implementing a centralized embedded enterprise resource planning (ERP) solution powered by Dynamics 365 Business Central and Suite Engine’s integrations, rather than through additional “add-on” tools or middleware layers, may address these structural issues at their core.
The Real Cost of Running Your eCommerce Channels in Separate Systems
The financial impact of operating multi-channel eCommerce through disconnected systems extends far beyond the administrative cost of your accounting team's time. It also affects their ability to support strategic decision-making for the business. According to Cherry Bekaert’s 2025 Middle Market CFO Survey, almost half of respondents reported a lack of integration between systems as their top challenge.
Specific to the retail industry, the lack of unified multi-channel inventory management and order synchronization is challenging and leads directly to revenue leakage, marketplace penalties and significant inventory distortion.
Inventory distortion costs retailers an estimated $1.6 trillion annually, according to Meteor Space, while Firework found that stockouts alone account for 40% of lost sales, as customers switch to competitors when items are unavailable. Additionally, poor inventory management causes businesses to lose up to 11% of their annual revenue.
Another risk of disparate multi-channel channels is overselling. For example, you risk overselling when an item sells on your Shopify store, but your Amazon and WooCommerce storefronts do not reflect that reduction in available stock based on your configured sync schedule. Overselling on major marketplaces leads to immediate order cancellations, poor customer reviews, and ultimately, account suspensions or suppressed search rankings that devastate your primary revenue streams.
Yet despite these profound risks, relying on a single sales channel is not the most viable strategy. The key question for a CFO then becomes whether your underlying technological infrastructure can support this multi-channel growth without reducing margins, causing fulfillment errors or creating operational delays. Growth must stay within your capacity to manage it accurately; otherwise, is it really growth?
Why Generic Connectors and Middleware Fall Short for Multi-channel Retailers
Middleware Maintenance
To solve the fragmentation of multi-channel eCommerce, many mid-market retailers turn to standard eCommerce integration software. However, most integration tools on the market are structured as middleware — a separate software layer that sits between your core ERP and your various eCommerce platforms.
While it may initially seem like a straightforward bridge, middleware creates its own extensive maintenance requirements, adds another critical vendor dependency, and introduces an intermediary data translation step where errors, mismatched records and delays frequently occur.
Because each platform connector within a middleware solution may use entirely different data formats, different sync schedules and different fee structures, data is rarely harmonized. To address this, retailers frequently resort to common, yet highly inefficient workarounds:
- “Bolting on” separate, platform-specific connectors for each storefront
- Deploying standalone inventory management tools
- Exporting payment and settlement reports manually
- Hiring additional staff specifically to reconcile everything in Excel
This reactive approach creates the exact fragmentation and data silo problem the CFO was originally trying to solve.
Fulfillment Complexities
Generic multi-channel ecommerce integration also fails to adequately address severe fulfillment complexities. Consider the operational distinctions between these two fulfillment methods: Fulfillment by Amazon (FBA) and Fulfillment by Merchant (FBM).
These orders require entirely different handling protocols, inventory allocations and accounting treatments. Adding Multi-channel Fulfillment (MCF) — using your FBA inventory to fulfill non-Amazon orders from platforms like Shopify or BigCommerce — adds yet another intricate layer of data routing.
Without an integration solution that natively understands these distinct logistics requirements, retailers are forced to manage these fulfillment routing decisions manually. This introduces human error into the fulfillment pipeline, leading to misrouted orders, delayed shipping times and inaccurate cost-of-goods-sold (COGS) reporting.
When your multi-channel ecommerce software relies on middleware, you are essentially maintaining three separate systems: the sales channels, the middleware layer and your ERP. For a finance leader, this translates into multiple points of failure during the financial close, compromised data integrity and a complete inability to trust the data without manual verification.
What Centralized eCommerce Integration Actually Changes
To achieve true operational efficiency and financial visibility, multi-channel retailers must move away from fragmented middleware and adopt a centralized, embedded approach. This approach enables you to:
- Operate in a single ERP environment
- Seamlessly convert orders from all channels
- Standardize all platform orders into a single format
Inventory availability updates systematically across all connected platforms based on your configured sync schedule, payment transactions post automatically to the correct general ledger (GL) accounts with precise fee detail, and financial reporting draws from one unified, authoritative data source instead of six separate dashboards. This is where specialized technology built within your ERP transforms the operation.
For multi-channel retailers running Microsoft Dynamics 365 Business Central, two solutions make this centralized approach possible.
Channel Sales Manager
Channel Sales Manager (CSM) by Suite Engine is fully integrated within Microsoft Dynamics 365 Business Central. CSM connects leading platforms, including Amazon, Shopify, BigCommerce, WooCommerce, Walmart, and Magento/Adobe, to a single ERP environment.
Crucially, CSM is embedded within Business Central, meaning it is not middleware. By operating entirely within your ERP, CSM eliminates the extra software layer, removing the translation errors and vendor dependencies associated with external integration tools.
Because it is embedded, CSM seamlessly converts platform orders into Business Central orders, which can then be fulfilled through various methods, including Amazon MCF. It respects the unique logistics of your operation. For example, CSM configures FBA and FBM orders differently based on their specific operational requirements, rather than forcing all fulfillment types into a single, generic workflow. Inventory availability updates from Business Central to your connected platforms based on your sync frequency, so that your available stock levels remain consistent across all digital storefronts, thereby protecting your seller reputation and maximizing revenue potential.
Channel Payments Manager
Equally critical for the CFO is managing complex payment data. Channel Payments Manager (CPM) by Suite Engine is designed specifically for payment processing within this ecosystem. CPM integrates payment platforms like Stripe and Usio directly into Business Central. When utilized alongside the CSM-CPM Connector, which ties eCommerce order data directly to corresponding payment transactions, CPM posts payment transactions, gateway fees and final payouts to the correct GL accounts as part of the payment capture workflow.
For the CFO, the benefits of this embedded architecture are transformative. You gain consolidated multi-channel financial reporting directly from one system. Because CSM posts fees at the transaction level, it enables detailed profitability analysis by channel, allowing you to see exactly how marketplace fees, shipping costs, and payment processing charges impact your bottom line for every order. You achieve strict inventory accuracy across all storefronts, sophisticated fulfillment coordination (including Amazon MCF), and the complete elimination of manual reconciliation between disparate platform dashboards.
5 Questions Every Multi-channel Retailer CFO Should Ask Before Choosing Technology
Evaluating multi-channel ecommerce software requires a critical look at how the technology interacts with your core financial processes. Before investing in a new system or attempting to optimize your current stack, CFOs should use these five practical evaluation criteria to assess their infrastructure:
1. Can the system consolidate orders from all your sales channels into a single ERP environment, or are you managing separate connectors and data formats for each platform?
If your team is managing different data formats for Shopify, Amazon, Walmart, etc., your accounting system is effectively speaking multiple languages. A true enterprise solution must ingest diverse marketplace data and standardize it into a single, unified order format within your ERP. This consolidation serves as the foundation for automated order processing and streamlined financial reporting.
2. Does the integration handle the differences between fulfillment types (FBA, FBM, Multi-channel Fulfillment), or does your team manage those distinctions manually?
Fulfillment is not a one-size-fits-all process. The accounting treatment for inventory held at an Amazon fulfillment center (FBA) differs significantly from inventory held in your own warehouse (FBM). Furthermore, leveraging Amazon MCF to fulfill a Shopify order requires sophisticated data routing. If your system does not inherently recognize and configure these differences automatically, your operations team will be forced to perform manual interventions that delay shipping and obscure true fulfillment costs.
3. Can you see transaction-level fee data from each platform in your general ledger, or is your team exporting payment reports and reconciling them in spreadsheets?
Marketplaces and payment gateways rarely deposit gross sales into your bank account; they deposit net payouts after deducting a complex array of listing fees, commission rates and processing charges. If your system only records the net deposit, you lose all visibility into your actual expenses. Your technology must be able to parse settlement reports and post fees at the transaction level to the proper GL accounts, allowing your finance team to close the books efficiently without days of spreadsheet reconciliation.
4. Is the integration embedded within your ERP, or is it a separate middleware layer that requires its own maintenance, licensing and vendor relationship?
Middleware introduces latency, potential data translation errors and additional IT overhead. When an integration is embedded within Dynamics 365 Business Central, it leverages the native business logic of your ERP. This eliminates the gap where data often gets lost between the marketplace and the accounting system, reducing your overall technology footprint and simplifying vendor management.
5. Can you report on channel-level profitability, inventory position, and fulfillment status from a single system, or are you assembling that picture from multiple sources?
Strategic financial leadership requires rapid access to reliable data. If you cannot immediately determine whether your WooCommerce channel is more profitable than your Amazon channel after accounting for all fees and fulfillment costs, your ability to allocate capital effectively is severely impaired. True multi-channel inventory management and financial oversight require a single source of truth that only a centralized ERP integration can provide.
How Cherry Bekaert Helps Multi-channel Retailers
Navigating the transition from multiple fragmented systems to a unified, centralized ERP environment requires both deep financial acumen and technical experience. Cherry Bekaert stands as your trusted advisor in this arena, offering a powerful combined advisory and technology capability tailored to the complexities of mid-market operations.
Through our CFO Advisory Services, we help finance leaders define their overarching operational strategy, identify areas of revenue leakage and establish robust financial reporting frameworks. Concurrently, our Digital Advisory professionals and technologists manage the detailed evaluation, meticulous planning and seamless implementation of the systems required to execute that strategy.
Your Guide Forward
If your finance team is struggling with manual reconciliation, fragmented data and limited channel visibility, it is time to modernize your infrastructure. Connect with a Cherry Bekaert professional for a strategic conversation about your digital retail operations, or explore the specific capabilities of CSM and CPM by Suite Engine to see how technology powered by Dynamics 365 Business Central can transform your multi-channel eCommerce business.
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