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The Biggest Challenges in eCommerce Migration and How to Avoid Them

Feb 28, 2025 • 17 min

Introduction

In the world of ecommerce, change is inevitable. Customer expectations, market demands, and technological advancements are constantly evolving, pushing businesses to adapt—or risk falling behind. For many companies, this means undertaking an ecommerce migration, a process that involves moving their online store to a more scalable and modern platform, usually without major changes to architecture. Done right, ecommerce migration is an opportunity for growth, offering better performance, security, and improved user experience.

Recent data highlights the growing importance of ecommerce platform modernization. The eCommerce Platforms Report states that 61% of B2B ecommerce sellers plan to migrate to a new platform within the next 12 months, citing outdated systems as a key barrier to growth. And merchants’ expectations of the cost of switching platforms vary widely, with the majority planning to spend between $25,001 and $500,000.

This guide for an ecommerce migration will walk you through everything you need to know, from planning and strategy to overcoming common challenges. Our ecommerce migration whitepaper also explores best practices, practical checklists, and how the right ecommerce migration services can help you navigate this critical transition. If you’re considering migrating to Shopify, Magento, or Virto Commerce, you’ll find insights here to make it a success.

Looking to modernize your ecommerce platform? Check out our eCommerce Re-platforming,  and How to Choose an eCommerce Platform guides to get started!

What is eCommerce Migration?

eCommerce migration refers to the process of transferring an online store from one platform to another, often driven by the need for better performance, scalability, and modern features. This transition touches every aspect of an online business—from the product catalog and customer information to SEO rankings, custom integrations, and user experience.

Companies typically consider ecommerce site migration when their current platform no longer meets business needs, whether due to technological limitations, high operational costs, or poor site performance. A Deloitte article that surveyed B2B companies reports their number one priority for technology investment is a new or upgraded ecommerce platform.

Additionally, a Deloitte Private survey from 2024 found that increasing AI use across the organization (43%) and investments in technology (37%) are the top two business priorities for private companies over the next 12 months.

Why Is eCommerce Migration Important?

eCommerce migration is more than a technical upgrade—it’s a strategic move that directly impacts business growth. Here’s why it’s crucial:

  • Scalability and Performance: Modern platforms handle increasing traffic and larger product catalogs more efficiently, ensuring your store remains fast and responsive even during peak periods.
  • Improved UX: Faster loading times, modern design capabilities, and AI-driven personalization tools contribute to a better shopping experience that keeps customers engaged.
  • Competitive Advantage: Migrating to a robust platform allows businesses to stay ahead by adopting advanced features and integrations, such as marketing automation, omnichannel capabilities, and headless commerce.
  • Better Security and Compliance: Outdated platforms often lack the security protocols necessary to protect sensitive customer data. Newer solutions offer built-in security measures and compliance with industry standards.
  • Cost Efficiency: High maintenance costs associated with legacy systems can weigh down business growth. Migration to a cloud-based ecommerce solution reduces costs by eliminating the need for expensive on-premises infrastructure.

Failing to migrate at the right time can lead to missed opportunities, frustrated customers, and costly workarounds to keep an outdated system running. 

Common Reasons for eCommerce Migration

eCommerce migration is not a decision businesses take lightly. It’s often driven by necessity rather than convenience. As companies grow, limitations in current ecommerce platforms become apparent, prompting the need for a more robust solution. Below are the most common reasons why businesses decide to migrate their ecommerce platforms.

1. Outgrowing the Current Platform

Deloitte's insights emphasize the importance of modernizing ecommerce platforms to enhance customer experience and maintain competitiveness in the digital marketplace. Growth is definitely essential in ecommerce, but rapid expansion can push a platform beyond its limits. Businesses that started with a basic solution often find it unable to support their growing traffic, extensive product catalogs, and increasing complexity.

For example, platforms that cannot efficiently handle hundreds of thousands or even millions of SKUs may experience performance issues, slowing down site responsiveness and impacting the customer experience. This scenario is common in industries where products come in numerous variations, such as size, color, and material.

Take Caplugs, for instance. Although the product range may appear limited at first glance, the company’s catalog includes nearly 2 million items, with each product often available in dozens of variations. In such cases, scalability becomes a critical factor, as only advanced ecommerce platforms can manage such complex and large-scale inventories without compromising performance.

2. Performance and Speed Issues

A slow site is a conversion killer. Studies indicate that 53% of mobile site visits are abandoned if pages take longer than 3 seconds to load. Additionally, research has shown that pages that loaded in 2.4 seconds had a 1.9% conversion rate, which decreased to 0.6% when load times reached 5.7 seconds.

Poor performance not only frustrates customers but also leads to lost revenue. For instance, over 1 in 10 business owners (12%) reported losing revenue every month due to poor website performance, averaging an annual loss of $20,172, or 15% of their total revenue.

If your current platform struggles to handle high traffic or spikes in demand, such as during Black Friday sales, it's crucial to consider migrating to a platform with better performance capabilities. Implementing strategies like load balancing, caching, and scalable hosting solutions can help maintain optimal website performance during peak traffic periods.

3. High Maintenance Costs and Total Cost of Ownership (TCO)

Legacy platforms often come with hidden costs—licensing fees, frequent maintenance, and expensive updates. Over time, the total cost of ownership can far exceed the initial investment. Migrating to a modern, cloud-based ecommerce platform can significantly reduce these costs while improving overall efficiency.

For example, Gartner has highlighted that organizations without effective cloud cost optimization strategies may overspend on cloud services by up to 70%, often due to overprovisioning and inefficient use of resources.

4. Limited Integration Capabilities

Modern ecommerce operations rely on seamless integrations with third-party services such as payment gateways, CRM systems, and inventory management solutions. Older platforms may lack the flexibility to integrate with essential tools, limiting business growth opportunities.

5. Gaps in Functionality and User Experience

eCommerce platforms must evolve with customer expectations. If your platform doesn’t support omnichannel selling, advanced personalization, or mobile-optimized experiences, you risk losing customers to competitors. Businesses that prioritize customer experience often see higher retention and conversion rates.

Investing in UX/UI design is crucial. According to Forrester Research, a well-designed UI can increase a website's conversion rate by up to 200%, and a better UX design can yield conversion rates up to 400%.

6. Administrative Complexity and Poor Internal Tools

A clunky admin interface can slow down your team, creating inefficiencies and frustration. If routine tasks like managing product catalogs or processing orders take too long, migrating to a platform with a more intuitive backend can greatly improve productivity and morale. Modern platforms with no-code or low-code interfaces enable non-technical staff to perform updates and tasks without IT support.

7. Security and Compliance Risks

Outdated platforms are often vulnerable to security breaches and lack compliance with the latest data protection regulations, such as GDPR. Migrating to a platform with built-in security measures ensures that sensitive customer data remains protected.

When is the Right Time to Migrate?

Recognizing these pain points early is critical to avoid prolonged inefficiencies. If any of the challenges above sound familiar, it’s time to evaluate your current platform and consider migrating.

Considering migration?

Explore our eCommerce Re-platforming Guide and discover how Virto Commerce can help you overcome these challenges.

How to Plan an eCommerce Migration

Without a solid plan, you risk costly errors, data loss, and extended downtime. However, with the right strategy and team in place, you can turn this transition into an opportunity for growth.

Step 1: Assessment and Preparation

The first step in planning your migration is to assess your current ecommerce platform and business needs.

  1. Define business goals: Start by answering the why behind the migration. Business goals should focus on outcomes like growing revenue, reducing operational costs, capturing or retaining market share, or entering new markets. Once these strategic goals are clear, technical objectives—such as improving performance or integrating new tools—can be aligned accordingly.
  2. Audit your existing platform: Evaluate how well your current platform supports your business goals. Are performance issues affecting sales? Are there functionality gaps limiting growth opportunities or market expansion? Identifying these limitations will help you determine what’s required from the new platform.
  3. Analyze key metrics: Assess critical data points such as conversion rates, site traffic, average order value (AOV), and bounce rate. These insights will guide you in setting measurable post-migration goals and tracking the success of the new platform.
  4. Inventory your data: At this stage, focus on evaluating your data to understand what needs to be migrated. Identify essential product descriptions, customer records, and order histories. The actual data cleansing and standardization should occur later, once the target data structure for the new platform is defined.

Gartner has reported that 83% of data migration projects either fail outright or exceed their allotted budgets and implementation schedules. This high failure rate underscores the critical importance of thorough data preparation and review in migration projects. Inadequate data quality and lack of proper planning are significant contributors to these failures.

Step 2: Choose the Right Platform

Choosing the right ecommerce platform is one of the most critical decisions in the migration process. Consider factors like customization, integration options, and long-term costs.

Popular Platforms: Shopify, Magento, and Virto Commerce offer a range of solutions for different business needs. Virto Commerce, for instance, is designed for B2B ecommerce, offering flexibility, headless commerce capabilities, and seamless third-party integrations.

Tip: Create a Request for Proposal outlining your requirements and invite vendors to provide detailed solutions. Schedule demos with your top 3 choices to assess how well each platform aligns with your business goals.

Checklist for platform selection:

  • Does it offer the scalability you need for future growth?
  • Can it integrate with your CRM, ERP, and payment gateways?
  • What is the Total Cost of Ownership over the next 3–5 years?
  • Does it meet your security and compliance requirements?
  • How adaptable is the platform? Can it evolve with your business, supporting future innovations and adjusting to changing market demands?

By prioritizing adaptability alongside technical capabilities and costs, you make sure that the selected ecommerce platform will continue to meet your needs as your business grows.

Need help with platform selection?

Read our How to Choose an eCommerce Platform guide for expert insights!

Step 3: Define an eCommerce Migration Strategy

There are two primary strategies for ecommerce migration:

  1. Big Bang Migration: All data and operations are transferred to the new platform at once. This approach is faster but riskier because any errors will affect your entire site. It’s suitable for smaller sites or those with limited data complexity.
  2. Phased Migration: The old and new platforms run in parallel for a set period. This strategy minimizes risks by allowing for extensive testing and gradual traffic shifts before the complete transition. While more time-consuming, it’s recommended for large, complex ecommerce operations. However, it’s important to note that this approach may not always be possible due to the limitations of the existing platform. Always consult your vendor to determine if they support phased migration and to understand any technical constraints that may affect the process.

 

Read more about these approaches in our Re-platforming guide

Data Transfer Methods:

  1. Manual Transfer: Suitable for small businesses with limited data.
  2. Automated Migration Tools: Many platforms offer built-in tools for seamless data transfer.

Step 4: Create a Migration Timeline

Break the migration into manageable stages, assign responsibilities, and define milestones. Avoid launching during peak sales periods to minimize customer impact. Plan for extra time to address unexpected issues and conduct final tests before going live.

Sample Migration Timeline

Stage 1: Data preparation and cleansing.
Stage 2: Platform configuration and integration.
Stage 3: Data migration and testing.
Stage 4: Full deployment and performance monitoring.

eCommerce Migration Checklist

A well-prepared checklist ensures you cover all aspects of the migration process:

  1. Complete a data backup: Protect your business by backing up all product data, customer information, and order history.
  2. Define roles and responsibilities: Assign a project manager to oversee the migration and ensure accountability across teams.
  3. Prepare an SEO strategy: Update URLs, create 301 redirects, and optimize metadata to preserve your search rankings.
  4. Develop a testing plan: Test every aspect of the new platform, from performance to functionality, before the final launch.
  5. Monitor post-migration performance: Track key metrics and customer feedback to identify and resolve issues quickly.

eCommerce Re-platforming Guide

Explore our guide for more in-depth tips and best practices for a successful migration! 

Common Challenges in eCommerce Migration

Migrating an ecommerce platform is a significant undertaking. While the benefits of a successful migration are substantial, the process itself is fraught with potential challenges that can disrupt your operations if not handled carefully.

1. Data Integrity and Security

Maintaining the accuracy and security of your data is one of the most critical aspects of ecommerce migration. Customer profiles, product catalogs, and order histories must be transferred without errors to avoid business disruptions. Even a minor data inconsistency can lead to customer dissatisfaction and lost sales.

Data security is equally vital, especially when handling sensitive information like customer payment details. The risk of data breaches can increase during these transitions if not properly managed. According to IBM's Cost of a Data Breach Report 2024, the global average cost of a data breach reached $4.88 million, a 10% increase from the previous year and the highest total ever recorded.

Key Security Risks:

  • Identity theft and unauthorized access.
  • Loss of sensitive business or customer data.
  • Compliance failures with regulations like PCI-DSS and GDPR.

Best Practices:

  • Use two-factor authentication (2FA) to protect sensitive areas of your platform.
  • Make sure all data is encrypted both in transit and at rest.
  • Audit your platform’s security settings and monitor for anomalies throughout the migration process.
  • Use automated tools for data validation to reduce human errors.

2. Downtime and SEO Impact

Even a few hours of downtime can cost ecommerce businesses thousands in lost revenue. In addition to revenue loss, poorly executed migrations can cause SEO rankings to plummet, especially if URL structures change without proper redirects.

Industry experts have observed that poor SEO planning during website migrations can lead to significant drops in organic traffic. For instance, an ecommerce migration case study highlighted a UK retailer experiencing nearly a 30% decline in organic traffic and over a 50% decrease in revenue for 3 consecutive months following a poorly executed migration.

Conversely, well-planned SEO migrations can prevent such losses and even lead to traffic gains. Another example describes a British ecommerce site that, after an initial brief downturn post-migration, achieved a 20% increase in organic traffic within a month and a 40% rise by the third month.

How to Avoid SEODisasters:

  • Set up 301 redirects for all affected URLs.
  • Conduct an SEO audit before and after the migration to track changes.
  • Monitor organic traffic and rankings closely for several weeks post-migration.

3. Integration and Customization Issues

Modern ecommerce platforms rely on integration with third-party systems like payment gateways, CRM, ERP, and marketing automation tools. However, many legacy systems may not integrate smoothly with the new platform, resulting in functionality gaps.

For example, an ecommerce business relying on custom APIs for inventory management may find that these APIs need to be rewritten or updated to work with the new platform. Failure to plan for these integrations can delay the migration and increase costs.

Tip:

 

1. Map out all existing integrations and test their compatibility with the new platform.

2. Opt for well-supported third-party applications that offer frequent updates and reliable support.

3. Build custom solutions for unique business needs if necessary.

4. User Experience Disruptions

Any disruption of UX during migration—such as broken links, slow load times, or a poorly designed interface—can frustrate users and lead to lost sales.

UX Optimization Tips:

 

1. Test the entire customer journey on the new platform before going live.

2. Conduct A/B testing on critical elements such as the checkout process and product pages.

3. Continuously collect user feedback post-migration and make improvements based on data.

5. Post-Migration Monitoring

Migration doesn’t end when your new platform goes live. Continuous monitoring is essential to catch and fix issues that arise in the weeks following the migration. These issues can range from data discrepancies to unexpected bugs that affect the shopping experience.

Monitoring Strategy:

  • Set up analytics and error tracking tools to monitor site performance.
  • Review and update internal and external links regularly.
  • Create a support plan for post-migration issues to resolve them quickly.

Summary of the Best Practices for eCommerce Migration

1. Plan Thoroughly

Begin with an analysis of your current ecommerce environment. Identify existing limitations, desired features, and set objectives for the migration. Develop a detailed roadmap outlining each phase, associated tasks, and timelines.

2. Develop a Data Backup Strategy

Prior to migration, implement a robust data backup plan. Secure all essential data, including product details, customer information, and transaction histories. Regular backups act as a safeguard against potential data loss during the migration process.

3. Pre-Migration Testing and Contingency Planning

Conduct testing in a staging environment before the full-scale migration. This includes validating data integrity, assessing website functionality, and ensuring compatibility with integrations. Additionally, establish contingency plans to address potential issues that may arise during the migration.

4. Maintain Customer Experience During Migration

To preserve a flawless customer experience, schedule migrations during periods of low traffic. Communicate any anticipated downtime or changes to your customers in advance. Post-migration, monitor the site closely to promptly address any user-reported issues, providing uninterrupted service.

5. Utilize AI-Powered Tools

Leverage AI-driven tools and collaborate with specialized agencies to facilitate the migration process. AI can assist in data mapping, predictive analytics, and automating repetitive tasks. Partnering with experienced agencies provides access to expertise and resources that can further facilitate your transition.

6. Be Ready for a Sales Increase

A survey conducted in the first half of 2024 revealed that one third of respondents reported sales increases of 30% or more after migrating ecommerce platforms. Make sure your team is prepared to handle additional demand by scaling your operations, optimizing inventory management, and reinforcing customer support.

Solutions and Services for eCommerce Migration

Partnering with a reliable ecommerce migration agency can significantly improve your chances of success. From data migration to platform integration, these experts help manage the complexities of migration. Key services offered by top ecommerce migration agencies include:

  • eCommerce Data Migration Services: Accurate and secure data transfer, including product information, customer profiles, and order history.
  • eCommerce Platform Migration Services: Transitioning from outdated ecommerce systems to modern, scalable platforms.
  • eCommerce Website Migration Services: Ensuring a seamless transition while preserving SEO rankings and providing a superior user experience.

Tip: Choosing an agency with experience in your industry and familiarity with your existing technology stack is crucial for a successful migration.

Tools for eCommerce Migration

Choosing the right tools can simplify the migration process and reduce risks. Here are some popular solutions:

Automated migration tools: Can simplify the transfer of standard datasets such as product catalogs, customer information, and order histories. However, these tools are typically most effective for off-the-shelf solutions that have not been extensively customized. Fo example, LitExtension, known for its user-friendly interface and support for over 120 ecommerce platforms, provides a data transfer experience for simpler ecommerce migrations.

ETL (Extract, Transform, Load) Tools: For complex ecommerce migrations, ETL tools offer greater flexibility by enabling customized data mapping, transformation, and validation. These tools are particularly useful when migrating from highly customized systems where data structures differ significantly between the source and target platforms. For instance, Talend Data Integration offers advanced data mapping, cleansing, and transformation features, ensuring high-quality data migration for large and complex ecommerce projects.

Why Choose Virto Commerce for eCommerce Migration?

Virto Commerce, founded in 2011, is a global leader in B2B ecommerce and marketplace solutions. We specialize in highly customizable headless commerce platforms that empower businesses to innovate and transform digitally.

At the core of our offerings is the Commerce Innovation Platform, powered by our proprietary Virto Atomic Architecture™ and Virto Cloud, which deliver flexibility for businesses to scale and adapt to market demands & customization to create high-performance digital experiences.

Virto Care: Post-Migration Support

We understand that migration is just the first step. With Virto Guarantee, our dedicated support program, we will make sure your business continues to thrive. We provide:

  • Monitoring and optimization to maintain performance.
  • Access to expert support teams who address technical challenges swiftly.
  • Regular updates and proactive improvements to your ecommerce platform.

We are trusted by global enterprises such as HEINEKEN, Hyundai, Bosch, De Klok Dranken, and Standaard Boekhandel. We don’t just provide adaptable ecommerce technology; we partner with our customers on their digital transformation journeys.

Ready to discuss your ecommerce solution? Book a Demo!

Case Study: How De Klok Dranken Achieved 80% Digital Adoption

De Klok Dranken, a major beverage and food wholesaler for hospitality businesses in the Netherlands, needed a migration solution to replace their heavy SAP system. Their goal was to improve customer experience, boost digital adoption, and stay ahead of growing competition.

De Klok chose the Virto Commerce platform and partnered with Innovadis, a leading technology integrator. Virto’s headless and modular architecture enabled easy integration with existing tools, providing data import/export capabilities and laying the foundation for continuous innovation.

The Results:

  • The solution was deployed in just a few weeks.
  • 80% of De Klok’s vendors are now served through the platform.
  • The company achieved the fastest time-to-value and continues to add new functionalities.
  • Today, De Klok is the leading beverage distributor in its sector with a general adoption rate of 80%.

Read the full De Klok Dranken success story here!

Looking for the same level of success with your ecommerce store? Virto Commerce offers future-ready, adaptable technology and expert guidance to help businesses like yours thrive. Partner with us to achieve ecommerce excellence!

Conclusion

eCommerce migration is an investment in your business’s future. A well-planned migration can lead to better performance, customer experience, and scalability.

For large-scale ecommerce migration, trust Virto Commerce. Our tailored solutions ensure a smooth and secure transition.

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