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- API versioning creates confusion with outdated examples, especially with a search result!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
Why This Persists:
Shopify's architecture was designed for single-store simplicity. Multi-store functionality would require fundamental platform restructuring.
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
Trade-offs to Consider:
- Increases complexity and ongoing management overhead. 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
Why This Persists:
Rate limits protect platform stability, but the complexity of GraphQL cost calculations makes them difficult to predict and manage.
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
Trade-offs to Consider: Over-optimization can lead to complex code that's harder to maintain.
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
Why This Persists:
Shopify focuses on simplicity over enterprise analytics complexity. Advanced reporting requires significant infrastructure investment.
Some Solutions:
- Third-Party Analytics Integration: Implement tools like Google Analytics 4, Klaviyo Analytics, or 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
- Performance Monitoring: Implement multiple data sources for cross-validation
Trade-offs to Consider: Third-party solutions increase costs and complexity but provide necessary insights for data-driven decision making.
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
Why This Persists: Shopify's app-first approach allows rapid feature expansion but creates dependency on external developers.
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
- Custom Development Assessment: Evaluate when custom solutions are more cost-effective; factor in maintenance costs
- Performance Monitoring: Implement tools to track app impact on site speed
Trade-offs to Consider: Custom development has higher upfront costs but provides more control and potentially better performance.
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
Why This Persists: Shopify prioritizes security and performance over complete customization freedom.
Some Solutions:
- 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
Trade-offs to Consider: Custom themes require higher initial investment and ongoing maintenance but provide maximum control.
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
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
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
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
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
Action Items:
- Share solutions across all teams
- Build internal knowledge base
- Use in client conversations to build trust
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
- Questions about specific limitations or solutions