Shopify Sucks! But Not Really
Top Challenges Facing Shopify Plus Merchants & How We Can Help
An opinionated, incomplete guide to Shopify Plus limitations (as of Sept 2025) and implementation solutions
Quick Wins: The "Easy" Problems
These get talked about everywhere, but they're mostly solved
Recently Fixed or Manageable:
100 variant limit per product(expanding to 2,048 in 2025)- SEO & URL Structure Rigidity -> "Get over it". Google knows how to parse a Shopify storefront.
- Limited native B2B features -> Shopify Plus B2B tools are rapidly improving; though not viable for complex wholesale operations. Recommend they wait (or really draw out the discovery process😜)
- Transaction fees when not using Shopify Payments - this will likely never change. If it's a dealbreaker, then that's that.
Key Point:
If prospects only bring up these issues, they haven't done their homework. The real challenges are deeper.
Documentation & Developer Experience
🎯 Technical Platform
The Problem:
- Documentation appears comprehensive but lacks critical implementation details
- Missing context on edge cases, limitations, and real-world scenarios
- Developers frequently resort to Stack Overflow, forums, and blog posts to fill gaps
- API versioning creates confusion with outdated examples, especially with a search result!
Why This Persists:
Shopify prioritizes rapid feature development over comprehensive documentation maintenance. With quarterly API releases, keeping docs current across all use cases is challenging.
Some Solutions:
- Build relationships with Shopify Plus support for direct technical clarification
- Maintain internal documentation library with real-world examples and edge cases
- Create a Shopify Technical blog series to spread street cred
- Create implementation checklists for common integration patterns
- Establish testing protocols to validate integrations across API versions
Multi-Store Madness
🎯 Enterprise Scalability
"We need 7 international stores, but we want to manage them like one."
The Problem:
- No true multi-store management from single dashboard
- Independent stores require separate management for products, pricing, content
- Data synchronization between international stores is manual or requires expensive third-party solutions
- URL structure limitations force subdomain/separate domain approach vs. subfolder structure
The Shopify Markets Trap:
While Shopify Markets promises international expansion simplicity, it comes with significant drawbacks:
- Limited currency and pricing control - can't set unique pricing strategies per market
- Tax complexity becomes a nightmare with multiple jurisdictions
- Shipping configuration doesn't handle complex international logistics well
- Content localization is basic compared to dedicated regional stores
- Performance issues - single store serving global traffic creates latency
- SEO limitations - subfolder structure isn't always possible, hurting regional search rankings
Why This Persists:
Shopify's architecture was designed for single-store simplicity. Multi-store functionality would require fundamental platform restructuring. Markets was their attempt to solve this without architectural changes.
Some Solutions:
- Organizations: Nearly all Shopify Plus merchants should be set-up as an Organization, which allows for multiple stores.
- PIM/OMS Integration Strategy: Implement tools like Salsify, Akeneo, Jasper or similar to centrally manage product data
- Automation Scripts: Build custom tools for bulk operations across stores
- SKU-Based Relationships: Use consistent SKU structures to link products across stores
- Markets vs. Multi-Store Decision Framework: Evaluate complexity of pricing, tax, and content needs before choosing approach
Trade-offs to Consider:
- Markets = simpler setup, limited flexibility, potential performance issues
- Multi-store = complex management, higher costs, maximum control
- PIM solutions are expensive but often necessary at scale
- 🤔Can an I18N solution work instead?
API Rate Limit Russian Roulette
🎯 Technical Platform
"Our integration worked for the last nine months, why did it suddenly break in late November?"
The Problem:
- GraphQL query cost calculations are complex and unpredictable
- Standard plans have restrictive API limits (Shopify Plus gets 10x increase)
- REST API is being deprecated, forcing GraphQL adoption
- Integration testing becomes challenging with rate limiting
- Black Friday traffic spikes can trigger unexpected rate limiting even for Plus merchants
Why This Persists:
Rate limits protect platform stability, but the complexity of GraphQL cost calculations makes them difficult to predict and manage. Holiday traffic creates unpredictable load patterns.
Some Solutions:
- Query Optimization: 🚨Design efficient GraphQL queries to minimize costs🚨
- Caching Strategies: Implement robust caching to reduce API calls
- Monitoring Tools: Implement API usage tracking and alerting
- Holiday Preparation: Load test integrations before peak seasons
- Fallback Strategies: Design graceful degradation when rate limits are hit
Trade-offs to Consider: Over-optimization can lead to complex code that's harder to maintain. Holiday preparation requires significant testing overhead.
Analytics & Reporting Limitations
🎯 Business Intelligence
The Problem:
- 1,000-row limit on reports requires exports for larger datasets
- Basic analytics lack enterprise-level insights (cohort analysis, LTV calculations)
- Attribution tracking struggles with multi-channel campaigns
- Real-time data delays during peak periods (12-24 hours)
- Cannot customize dashboards for specific KPIs without third-party tools
- GA4 confusion - many clients are overwhelmed by the transition from Universal Analytics
Why This Persists:
Shopify focuses on simplicity over enterprise analytics complexity. Advanced reporting requires significant infrastructure investment. Google's GA4 rollout created industry-wide confusion.
Some Solutions:
- GA4 Alternatives for Confused Clients:
- Triple Whale - e-commerce focused, easier interface than GA4
- Northbeam - advanced attribution for larger businesses
- Klaviyo Analytics - excellent for email/SMS driven businesses
- Glew - purpose-built for e-commerce reporting
- Third-Party Analytics Integration: Implement specialized e-commerce BI tools
- Custom External Reporting: Build automated reporting using Shopify's API combined with external data sources
- Data Warehouse Integration: Sync Shopify data to tools like BigQuery, Snowflake, or Datalake for advanced analysis
- GA4 Training & Setup: Provide proper GA4 configuration and training to bridge the knowledge gap
Trade-offs to Consider: Third-party solutions increase costs and complexity but provide necessary insights for data-driven decision making. Multiple analytics tools can create conflicting data stories.
App Ecosystem Spiral
🎯 Platform Architecture
"We need 23 apps to run our store, and they cost more than Shopify"
The Trap:
- Core business functions often require paid third-party apps
- App conflicts compound over time and poorly built apps can slow a site
- Subscription costs for multiple apps can exceed platform costs💰
- No control over app quality and ongoing maintenance
- App integration gaps - getting apps to talk to each other is often impossible
Real-World App Landscape: The Good:
- Hulk Apps - decent quality, broad functionality, reasonable pricing
- Klaviyo - industry-leading email/SMS platform with robust integrations
- Algolia - excellent search initially, but...
The Problematic:
- Algolia scaling issues - works great until you need complex features, then falls apart quickly
- Integration nightmares - product recommendation apps that can't talk to review apps
- Performance degradation - multiple apps loading scripts creates cumulative slowdown
Why This Persists: Shopify's app-first approach allows rapid feature expansion but creates dependency on external developers. Apps are built in silos without integration standards.
Some Solutions:
- App Audit Strategies: Regular review of app necessity and performance impact - a great part of QBR cycle
- Consolidation Opportunities: Choose multi-functional apps over single-purpose solutions; or multiple apps from the same dev
- Integration Testing: Specifically test app-to-app compatibility during selection
- Performance Monitoring: Implement tools to track app impact on site speed
- Custom Development Assessment: Evaluate when custom solutions are more cost-effective; factor in maintenance costs
- Vendor Relationship Management: Prioritize apps from developers with good support track records
Trade-offs to Consider: Custom development has higher upfront costs but provides more control and potentially better performance. App consolidation may sacrifice best-in-class functionality for simplicity.
Content Management & Page Building Limitations
🎯 Design & User Experience
The Problem:
- Basic blogging platform lacks features compared to WordPress or dedicated CMS
- Limited content organization tools (tagging, categorization)
- No advanced SEO settings for individual blog posts
- Limited ability to create complex layouts and content structures
Why This Persists: Shopify prioritizes e-commerce functionality over content management. Adding full CMS capabilities would increase platform complexity and maintenance overhead.
Some Solutions:
- Premium Page Builder Apps: Implement Shogun, PageFly, or GemPages for advanced page building
- Blog Enhancement Apps: Add SEO Blog Optimizer or similar tools for better blog functionality
- Custom Content Tools: Develop custom metafield-based content management systems
⚠️This can be very challenging for a Marketing team to maintain⚠️
Customer Support Escalation Lottery
🎯 Operations & Support
The Problem:
- Technical issues often require multiple escalations to reach qualified support
- Non-Plus merchants experience longer response times and limited technical support
- Support team cannot assist with checkout.liquid or deprecated feature issues
- Knowledge gaps between general support and technical implementation needs
Why This Persists: Shopify's massive scale (4.5+ million stores) makes personalized technical support challenging for all merchants.
Some Solutions:
- Partner Support Relationships: Build those relationships with the internal Shopify team
- Be a Billion Dollar Company: no really, be too big to be ignored
Trade-offs to Consider: Partner relationships and internal capabilities require investment but provide more reliable support.
Theme & Customization Constraints
🎯 Design & User Experience
The Problem:
- Dynamic sections limited to homepage on many themes
- Custom fields require apps or complex metafield management
- Limited customization or lots of coding overhead: pick one
- Theme updates for purchased themes can break customizations
The Discovery Dilemma: How do you identify during discovery whether a prospect will:
- Need too much customization for a purchased theme to work
- Want too much customizability to reasonably build a purpose-built theme
Red Flags in Discovery:
- "We want it to look exactly like [completely different platform]"
- "Can we change the checkout flow?" (spoiler: very limited options)
- "We need custom product configurators" without budget for custom development
- "We want to be able to edit everything ourselves" + complex design requirements
Why This Persists: Shopify prioritizes security and performance over complete customization freedom.
Some Solutions:
- Customization Scope Assessment: Develop discovery questions that reveal customization expectations early
- Theme vs. Custom Decision Matrix: Create clear criteria for purchased vs. custom theme recommendations
- Client Education: Show examples of what's possible within theme constraints vs. custom development
- Custom Theme Development: Build bespoke themes for clients requiring extensive customization
- Metafield Strategy: Implement ‼️structured‼️ approach to custom data management
- Version Control: Maintain proper theme versioning and backup strategies (Tricky build system👍)
- Progressive Enhancement: Layer customizations that survive theme updates
Discovery Questions to Ask:
- "Show me 3 websites you love and want to emulate"
- "What specific functionality does your current site have that you can't lose?"
- "Who will be maintaining the site content day-to-day?"
- "What's your timeline and budget for custom development?"
Trade-offs to Consider: Custom themes require higher initial investment and ongoing maintenance but provide maximum control. Purchased themes limit flexibility but speed deployment and reduce costs.
Turning Problems Into Profits
For Sales Teams
- Set Clear Expectations: Discuss these limitations during discovery to avoid surprises
- Position The Value: Emphasize experience navigating these challenges
- Competitive Advantage: Use existing solutions as differentiators against other agencies
- Discovery Framework: Use limitation discussions to uncover true project scope and budget needs
For Account Managers
- Proactive Communication: Address potential issues before they impact client operations
- Solution Roadmaps: Present clear timelines and resource requirements for complex implementations
- Ongoing Partnership: Position ongoing support as essential for Shopify Plus success
- Client Education: Help clients understand when they're asking for the impossible vs. expensive
Turning Problems into Resumes
For Project Managers
- Risk Assessment: Build these challenges into project planning and timelines
- Resource Allocation: Ensure adequate technical resources for complex implementations
- Testing Protocols: Implement comprehensive testing strategies, especially for app integrations
- Scope Management: Use limitation knowledge to prevent scope creep
For Engineers
- Best Practices: Develop standardized approaches to common Shopify Plus challenges
- Documentation: Maintain internal knowledge base for implementation patterns
- Continuous Learning: Stay current with Shopify's evolving API and platform changes
- Integration Expertise: Become the person who knows which apps work well together
The Bottom Line
Shopify Plus is powerful, but knowledge of its limits is where the competitive advantage plays in
Key Takeaways:
- Every limitation = opportunity to demonstrate expertise
- Proactive communication prevents client surprises
- Our solutions differentiate us from other agencies
- Ongoing partnership is essential for Shopify Plus success
- Discovery is where you win or lose projects - use limitation knowledge to scope properly
Action Items:
- Share solutions across all teams
- Build internal knowledge base of app compatibility
- Develop discovery questions that reveal customization scope
- Create decision frameworks for Markets vs. multi-store
- Use in client conversations to build trust and set proper expectations
Questions & Discussion
What challenges have you encountered that we should add?
Discussion Topics:
- Client stories and solutions you've implemented
- New challenges emerging with recent Shopify updates
- Tools and approaches that have worked well for app integration
- Discovery techniques that reveal true customization needs
- Questions about specific limitations or solutions