Shopify is the biggest name in the e-commerce space, and for good reason. The platform is relatively easy to set up, performs well, and has excellent marketing. Its app marketplace is constantly growing, adding more capabilities.

For many merchants, Shopify is all they need. Going with the market leader is an obvious choice.

However, when you reach an enterprise scale, with requirements for B2B commerce and increased operational complexity, the story becomes quite different. Shopify says they offer B2B capabilities at scale, and when you’re subjected to their marketing and advertised track record, it's easy to start nodding your head to the beat of their tune.

Let’s dive into the true cost of Shopify Plus. Reading this will help you ask the right questions and better equip you to judge the answers.

The Shopify Plus Sales Machine

When Shopify's enterprise sales team comes knocking, they arrive with a compelling story. They position Shopify Plus as the solution to all your B2B woes: lower total cost of ownership, enterprise features without enterprise overhead, and the promise that migrating to Shopify Plus will lead to a conversion rate boom.

But often these promises are unrealistic. The pitch typically centers around three key pillars that deserve closer scrutiny.

The conversion rate promise

Shopify's sales pitch often includes dramatic claims about conversion improvements—sometimes suggesting compounding monthly increases that would theoretically give you a 55% conversion rate within six months.

While speeding up your websites and simplifying checkout flows and payment processing can indeed help, they won’t help anything if people don't want your product. The fastest, most advanced checkout flow in the world won't magically increase your conversion rate. And conversely, if customers do want your product, one extra checkout step typically isn't the barrier preventing them from making a purchase.

This pitch also often centers specifically around Shop Pay, their wallet service that streamlines the checkout process. This can certainly grease the gears of B2C sales, fostering impulse buys and cross-selling with other merchants, but it’s often irrelevant to B2B customers who have different payment, invoicing, and pricing requirements.

Predictable pricing that might not be so predictable

Shopify Plus markets itself with predictable monthly pricing starting around $2,300-$2,500 per month. But this base fee is just the tip of the iceberg. What they don't emphasize up front are the hidden costs that can quickly multiply:

• Revenue share fees: Once you exceed $800,000 in monthly sales, you pay an additional 0.25% on incremental revenue
• Transaction fees: If you don't use Shopify Payments, you'll pay 0.15-0.20% per transaction
• Currency conversion fees: 1.5-2% on foreign currency transactions
• App ecosystem costs: Most B2B functionality requires third-party apps, often costing $500-$2,000+ monthly

The "It does everything" fallback

Perhaps the most dangerous aspect of the Shopify Plus pitch is the vague assurance that "it can do everything you need out of the box." They will probably say “yes” to everything. The truth is more nuanced. It has an app in the Shopify app store that might get you partway there, but they aren’t sure exactly what you mean by your requirements. And that app won’t be able to talk directly to other apps.

Chances are high that you won’t be satisfied, and you’ll need to invest in customization to get what you want.

Where Shopify Plus Falls Short for B2B Operations

Shopify Plus has several recurring pain points that go beyond feature gaps. They represent fundamental architectural limitations.

New customer accounts

One of the most glaring issues is Shopify's implementation of B2B customer accounts. The platform forces businesses to use "New Customer Accounts," which requires passwordless email verification for every login session. Users consistently complain about this. It’s not a very good UX for business buyers who reorder frequently.

Even worse, the system redirects users to an unbranded Shopify domain for authentication, completely breaking the customer experience flow. You can avoid the native B2B account system, but then you lose access to some of Shopify’s native B2B features.

Pricing flexibility

B2B commerce thrives on relationship-based pricing, contract terms, and customer-specific agreements. Shopify Plus struggles with this fundamental requirement. Although the platform has introduced B2B price lists, maintaining them is labor-intensive, and the system lacks the flexibility most B2B businesses require for complex pricing structures.

Want to offer automatic discounts to specific customers based on their contracts? You'll need workarounds involving Draft Orders or Shopify Functions—both of which have their own limitations and complexities. Out of the box, you simply can’t offer automatic discounts to specific customers.

Integration challenges

Here's where the "bolt-on" nature of Shopify's architecture becomes apparent. Unlike platforms built with extensibility in mind, Shopify's ecosystem lacks the interoperability that enterprise B2B operations require.

Consider a simple example: determining a customer's country based on their IP address for shipping calculations.

In Drupal, there's a de facto standard module (GeoIP detection) that every other module in the ecosystem can work with. In Shopify, each plugin or app might handle this differently—if at all—forcing you to hope that your shipping plugin has its own geo-detection built in. The wheel is reinvented half a dozen times.

This fragmentation leads to maintaining multiple apps that don't communicate well, duplicate data entry, and general confusion. Some B2B retailers are forced to use both Shopify's native B2B features and third-party pricing apps in parallel, leading to data inconsistencies and operational headaches.

A Total Cost of Ownership Example for Shopify Plus

When we calculate the real TCO for Shopify Plus B2B implementations, the numbers often surprise organizations that were attracted by the initial pricing.

Year one implementation costs

• Platform licensing: $24,000-$30,000 annually
• Custom development: $50,000-$150,000+ (theme customization, checkout scripts, integrations)
• Data migration: $5,000-$20,000+
• Third-party apps: $6,000-$24,000 annually

Range: $85,000 - $224,000.

If your business is in any way unique or your operations have evolved over a decade or more, expect a rate closer to the higher end of that range.

Ongoing hidden costs

• Transaction and processing fees: 2.15%+ on all sales, especially if not using Shopify’s built-in payment gateway (for invoicing or purchase orders, for example)
• Currency conversion: 1.5-2% on international transactions
• Revenue share: 0.25% on monthly sales above $800K
• Maintenance and support: $24,000+ per year for ongoing development
• Operational workarounds: Difficult to quantify but significant

For a B2B organization doing $5M annually in online sales, these costs can easily exceed $200,000 per year when everything is accounted for—significantly more than the $24K base license fee suggests.

The Hidden Cost of Platform Mismatch

Notice the “operations workarounds” line item above? That cost is harder to quantify, but you need to consider it when evaluating any platform. What operational friction emerges when your platform doesn't match your business reality? What is the ongoing cost of working around a system that wasn't built for how you actually operate?

Staff multiplication

When Shopify Plus can't handle your customer-specific pricing automatically, someone on your team becomes a human workaround. They manually adjust orders, issue refunds for pricing discrepancies, or spend hours maintaining complex spreadsheets to track contract terms that should be automated.

Not only does this increase upfront costs, but it also makes everything more prone to error, multiplying customer service issues.

On the other hand, a platform that aligns with your internal processes can save your staff hundreds of hours per month and reduce errors. This type of savings isn’t easy to quantify immediately but becomes more obvious as time goes on.

Technical debt

Every workaround you implement to address a platform limitation creates technical debt—code that works today but makes future changes more difficult and expensive.

Let's say you need customer-specific pricing, but Shopify's native B2B features don't quite meet your needs. You implement a patchwork solution using multiple apps and custom scripts. Six months later, when you need to add a new product line with different pricing rules, you discover that your workaround doesn't scale. Now you're not just implementing a new feature. You're refactoring the entire pricing system while trying to maintain business continuity.

We've worked with organizations where the accumulated technical debt from platform workarounds consumed 40-60% of their development budget. Every new feature expanded an increasingly fragile house of cards.

Innovation opportunity cost

The most strategic soft cost might be the opportunities you never pursue because your platform makes them too expensive or complex to implement. When every new feature requires extensive workarounds, you naturally become more conservative about innovation.

The platform that was supposed to enable growth becomes the constraint that limits it.

Quantifying the unquantifiable

How do you put a dollar figure on these soft costs? Start with time tracking. For one month, have your team log hours spent on:

• Manual order adjustments and corrections
• Customer service issues related to platform limitations
• Development time fixing platform-related bugs vs. building new features
• Administrative overhead from fragmented systems

What could your team accomplish if they weren't managing these workarounds? What new capabilities could you build? What customer experience improvements could you implement? While the exact cost varies by organization, it shouldn’t be ignored in your platform evaluations.

The "total cost of ownership" conversation must extend beyond the traditional three-year budget horizon. A platform that saves money in year one but constrains growth in years three through five may be the most expensive choice you can make.

When it makes sense to choose Drupal Commerce

Different businesses have different needs. Rather than forcing your processes into a predetermined mold, Drupal and Drupal Commerce provide a framework that can be composed to match your specific requirements. It’s truly composable and adaptable.

A typical cost structure for an initial site build: 

• Upfront investment: Higher initial development costs ($100,000-$200,000)
• Ongoing costs: Hosting, maintenance, and development support ($30,000-$100,000 annually)
• No percentage fees: No revenue sharing, transaction fees for platform usage, or app licensing costs
• Complete ownership: Your platform investment stays with you

When Drupal Commerce makes strategic sense

Consider Drupal Commerce when your B2B requirements include:

• Complex pricing structures: Multi-tier pricing, contract-based rates, or customer-specific agreements
• Deep system integration: ERP, CRM, or custom business systems that need tight coupling
• Specialized workflows: Quote-to-order processes, approval chains, or custom product configuration
• Global complexity: Multi-warehouse inventory, complex tax requirements, native multi-lingual and multi-currency support, or regional variations
• Content-heavy needs: Technical documentation, product specifications, or marketing content integrated with commerce

The Questions You Should Be Asking

Before making a platform decision, push beyond the marketing materials and ask some critical questions:

• "Can you show me exactly how [specific B2B requirement] works in your platform?" Don't accept vague assurances. Demand concrete demonstrations.
• "What's the total cost, including all apps, fees, and customizations needed for our requirements?" Get itemized pricing that goes beyond the base license.
• "How do we handle [your most complex business process] without workarounds?" If the answer involves multiple steps or manual intervention, calculate that operational cost.
• "What happens if we need to leave the platform?" Understanding exit costs and data portability is crucial for any long-term decision.
• "Who owns the customer relationship and data?" With Shopify Plus, you're essentially making Shopify a participant in your customer relationships through features like Shop Pay.

Making The Right Decision

The choice between Shopify Plus and Drupal Commerce isn't about which platform is "better.” Rather, which approach aligns with your organization's needs, capabilities, and strategic direction?

Choose Shopify Plus when:

• Your B2B requirements are relatively straightforward
• Speed to market is critical
• You prefer predictable SaaS costs over development investment
• You're willing to adapt some processes to fit the platform

Choose Drupal Commerce when:

• Your B2B processes are highly specialized
• Long-term cost control is more important than upfront investment
• Integration with existing systems is critical
• You need complete control over the customer experience

The Path Toward Strategic Platform Selection

The enterprise software landscape is littered with implementations that looked perfect in demos but failed to deliver in practice. The key to avoiding this trap is an honest assessment of your needs against platform capabilities. Don’t swallow marketing promises without first interviewing the cooks and inspecting the kitchen.

Shopify Plus can be an excellent choice for B2B organizations whose needs align with its strengths: a proven suite of basic features, rapid deployment, and managed infrastructure. But when your requirements push against the platform's limitations, the cost of workarounds and compromises can exceed the investment of a purpose-built solution.

The most expensive platform decision isn't the one with the highest upfront cost. It's the one that forces you to constantly work around its limitations, limiting your business agility and customer experience.

The right platform enables your business to grow and evolve efficiently while serving your customers effectively. Whatever you choose, make sure it's based on a clear-eyed assessment of both the capabilities and the costs, visible and hidden alike.