Common Problems When Migrating Websites Between SaaS Builders and CMS

Moving a website from one platform to another may look like a simple technical operation, but in reality, it is a complex and risky process that can affect every layer of your business. Migration between SaaS website builders (like Wix, Squarespace, or Shopify) and content management systems (such as WordPress, Drupal, or Joomla) is especially challenging. The difference in how these systems store, export, and interpret content often creates gaps that no one expects until it is too late.

For many organizations, migration becomes a turning point: some achieve greater flexibility and growth, while others face loss of traffic, broken layouts, and expensive fixes. Understanding the common problems before you start is the only way to prepare properly and minimize damage.

Why Website Migration Matters More Than You Think

Website migration is not just about moving files and content — it is about protecting visibility, revenue, and reputation. A single mistake during migration can wipe out years of SEO investment, break customer journeys, or cause downtime that directly affects sales.

For example, if redirects are not handled correctly, search engines may treat your new website as a completely different project, dropping it from the rankings. If your templates do not adapt, users may face broken layouts on mobile devices, making them leave instantly. If media libraries or blog posts do not transfer correctly, you may end up rebuilding months of work manually.

Migration matters because your website is more than a collection of pages. It is a digital asset that carries your brand identity, search authority, and customer trust. Treating migration as a strategic business move — not just a technical task — is the only way to protect what you’ve built.

What Makes SaaS to CMS Migration Especially Difficult?

SaaS platforms and CMS are built on completely different principles, and that gap makes migration inherently problematic. SaaS builders like Wix, Squarespace, or Shopify operate in closed ecosystems. They don’t give you full access to source code, databases, or raw files. Instead, you’re tied to their export tools — which are often limited, incomplete, or even locked down. By contrast, CMS platforms such as WordPress, Joomla, or Drupal give you nearly unlimited freedom, but that flexibility comes with technical complexity.

The friction between these two worlds creates challenges at every step: what you can export from SaaS often doesn’t align with what CMS needs to import.

Limited Export Capabilities

Most SaaS platforms restrict what you can take with you. Blog posts might export as XML, but categories, tags, and media files can be missing. Page layouts and templates usually don’t transfer at all. Even simple elements like navigation menus or internal links can be lost. This forces teams to rebuild large parts of the site manually.

Locked-In Design and Functionality

SaaS builders sell simplicity — drag-and-drop editors, pre-designed templates, and built-in features. But these elements rarely survive outside their ecosystem. A “gallery block” in Wix may have no direct equivalent in WordPress. A Shopify checkout flow may not map cleanly to WooCommerce. The result is broken design, missing features, or a need for costly redevelopment.

Technical Gaps Between Systems

SaaS platforms handle hosting, CDN, and caching automatically. When moving to CMS, these layers must be set up from scratch: choosing a host, configuring security, enabling backups, and optimizing performance. If overlooked, the new site can end up slower and less secure than the old one.

Hidden SEO Mismatches

Even before SEO migration is addressed directly, platform differences create risks. SaaS systems often generate clean but rigid URL structures, while CMS allows custom slugs. If these don’t match, existing backlinks and indexed pages can break. Meta tags, schema, and canonical references may not transfer correctly, leaving search engines confused.

The Business Impact

What makes SaaS-to-CMS migration so difficult isn’t just the technical mismatch. It’s the fact that every technical issue translates into real business consequences — downtime, lost traffic, higher costs, and frustrated customers. That’s why migration should be treated not as a “side project” but as a carefully planned operation.

SEO Risks You Can’t Ignore

Search engine optimization is the single most fragile part of any website migration. Years of work on rankings, backlinks, and authority can vanish in a matter of days if the process is not carefully managed. The danger is not theoretical — businesses regularly report losing 30–70% of their organic traffic after a poorly executed migration.

Redirects and Broken Links

The most common SEO disaster happens when URLs change but redirects are not set up properly. A page that used to rank on Google suddenly leads to a 404 error, and the search engine quickly removes it from the index. Even if redirects exist, chains or loops (301 → 302 → 301) can dilute authority. Every important page should map to a new destination with a clean, single-step 301 redirect.

Metadata and Structured Data Loss

Platforms often store metadata differently. Title tags, meta descriptions, and open graph data may be lost during export. More advanced elements — such as schema markup or canonical tags — are even less likely to transfer automatically. Without them, search engines may misunderstand the content or consider it duplicate, which harms rankings.

Sitemap and Indexing Problems

SaaS platforms typically generate and update sitemaps automatically. In CMS environments, you must configure plugins or tools to ensure the sitemap is correct and submitted to Google Search Console. A missing or outdated sitemap delays indexing, leaving new or migrated pages invisible for weeks.

Backlink Authority Risks

If your site has earned backlinks over time, every one of them points to a specific URL. Any change in structure can break those links, cutting off valuable authority. While redirects can preserve much of this power, they don’t fully transfer 100%. Each broken or redirected link represents a potential loss of SEO equity.

Duplicate Content and Canonicals

Migration sometimes creates multiple versions of the same content (for example, when importing blogs and categories separately). Without proper canonical tags, Google may index duplicates, splitting traffic and diluting relevance.

The Real Cost of SEO Errors

Unlike design or content issues, SEO mistakes often don’t show up immediately. You may see a slow decline in impressions and clicks weeks after migration, long after the project is considered “finished.” By then, recovering rankings is harder and often requires new campaigns, audits, and extra investment.

Bottom line: ignoring SEO during migration is not an option. It’s the single area where technical oversight translates directly into lost visibility, traffic, and revenue.

How Design and User Experience Break During Migration

Design and user experience are usually the first things clients notice after migration — and often the first source of disappointment. While SEO losses are hidden, broken layouts and clumsy navigation are painfully visible.

Templates Don’t Transfer One-to-One

SaaS builders rely on proprietary templates with drag-and-drop elements. These cannot simply be exported into a CMS like WordPress or Drupal. Instead, designers must rebuild layouts manually. Even with careful work, the final look may differ in spacing, typography, or animations. For brands with strict identity guidelines, these small mismatches can become big issues.

Widgets and Features Rarely Survive

Elements like galleries, forms, sliders, or booking modules are tied to the original SaaS ecosystem. Once migrated, they often disappear or must be replaced with third-party plugins. This not only requires configuration but can also create inconsistencies in style or functionality.

Responsive Design Breakdowns

A site that looked clean on mobile in Wix or Squarespace might look broken in WordPress if the theme isn’t optimized correctly. Buttons shift, text overlaps, or images scale poorly. Since mobile usability is both a ranking factor and a core part of user satisfaction, these design glitches can directly impact performance.

Navigation and Internal Linking Issues

Menus and navigation structures don’t always export smoothly. Missing or reordered menu items confuse users, while broken internal links frustrate them further. Beyond UX, this also harms SEO, as internal linking is a key signal for search engines.

The Hidden UX Cost

Design and UX issues don’t just make the site “look bad” — they affect real business outcomes. A confusing navigation flow can increase bounce rates. Poor mobile optimization can slash conversions. Even slight inconsistencies in branding may reduce trust, especially for eCommerce or B2B websites.

In short: during migration, design isn’t just about aesthetics. It’s about preserving the usability and trust that your audience already associates with your brand. Without a deliberate plan to rebuild templates and test user flows, the “new” website can feel like a downgrade rather than an upgrade.

Content and Structure Problems Every Migrant Faces

While SEO and design often dominate migration discussions, content and site structure bring just as many headaches. SaaS platforms and CMS handle content storage differently, which means the transfer is rarely seamless.

Blog Posts and Categories

Exporting blog posts usually works, but categories, tags, and authorship data often get lost in the process. For example, Squarespace can export posts into an XML file, but when imported into WordPress, categories may disappear, leaving all posts “uncategorized.” Rebuilding the taxonomy manually takes time and risks creating inconsistencies.

URL Slug Mismatches

SaaS builders often enforce rigid URL patterns, such as /blog/post-title. In CMS, slugs are flexible, but that flexibility means URLs may not match the originals. Even small differences — like /article/post-title instead of /blog/post-title — can break backlinks and harm SEO unless carefully redirected.

Media Libraries and Attachments

Images, videos, and documents are notorious for getting stuck. Some platforms allow image export, but the file paths change, leading to broken embeds. Other platforms restrict downloads altogether, forcing teams to manually re-upload media. This not only adds hours of work but can also bloat the site if not optimized properly.

Page Hierarchies and Navigation

SaaS builders often manage nested pages or navigation differently than CMS. A parent/child structure in Wix may not map directly into WordPress menus, creating missing or duplicated links. The end result is confusion for both users and search engines.

Internal Linking Challenges

When URLs and categories shift, internal links inevitably break. Blog posts that once linked to each other may now send users to 404 errors. Fixing this requires crawling the entire site with tools like Screaming Frog or Sitebulb to identify and repair broken paths.

The Human Cost of Content Gaps

Every missing image, broken URL, or lost category has to be fixed manually. For larger websites, that can mean days or weeks of rework. Beyond the labor cost, it creates a real risk of inconsistency: small details slip through, and the migrated site ends up messier than the original.

Bottom line: content is not just “text and images.” It’s the backbone of your site’s structure, and losing pieces of it during migration undermines both usability and authority.

The Hidden Business Risks Behind Migration

Most conversations about migration focus on technical checklists — redirects, templates, or content imports. But the real cost often shows up in business performance. When a website migration goes wrong, the impact extends far beyond broken pages. It can affect revenue, lead generation, and even customer trust.

Downtime and Lost Sales

During migration, even short periods of downtime can be damaging. An eCommerce store offline for just a few hours may lose thousands in revenue. Service businesses risk missing leads when forms don’t work or emails fail to send. Unlike technical bugs, downtime has a direct and immediate financial cost.

Unexpected Budget Overruns

Many companies underestimate the complexity of moving from SaaS to CMS. What starts as a “simple” project can quickly balloon into unexpected costs: hiring developers, buying plugins, or paying for design rebuilds. Worse, these expenses often come after the budget is already approved, creating tension between marketing and finance teams.

Damage to Brand Consistency

Migration isn’t just about moving code — it’s about protecting brand trust. If your new site launches with broken layouts, inconsistent fonts, or missing images, customers may view the brand as unprofessional. For organizations in B2B or high-trust industries (finance, healthcare, education), this can cause reputational harm that takes months to recover from.

Loss of Leads and Customer Data

Contact forms, CRMs, and email marketing integrations often break during migration. If forms stop delivering submissions or integrations fail, leads disappear without anyone noticing. Unlike traffic drops, these issues can remain invisible for weeks, silently draining the sales pipeline.

Long-Term Opportunity Costs

Even if the migration eventually succeeds, delays mean lost growth. While a marketing team fights technical fires, competitors continue to invest in campaigns, capture leads, and grow market share. The real cost is not only what is lost but also what is never gained.

In summary: business risks are the hidden layer of migration. Technical issues may be fixable, but lost revenue, broken trust, and wasted opportunities are much harder to recover. Treating migration as a strategic investment — not just a technical task — is the only way to protect both short-term and long-term performance.

How to Explain Migration Risks to Your CEO or Client

One of the hardest parts of migration is not the technical execution but the communication around it. CEOs, clients, and non-technical stakeholders don’t care about 301 redirects or schema markup. They care about traffic, leads, and revenue. The challenge is translating complex risks into clear business language.

Speak in Metrics, Not Jargon

Instead of saying “URL structures may not align,” explain it as: “If redirects aren’t handled, Google may stop sending us traffic to these pages, which could reduce leads by 30%.” Numbers and percentages make risks tangible and urgent.

Show Visual Impact

Simple before-and-after screenshots of traffic charts or mock-ups of broken layouts are often more effective than long explanations. Visuals help executives quickly grasp the potential damage.

Frame Migration as Investment, Not Expense

Highlight that migration is not just a technical cost but a business safeguard. Position it as protecting years of SEO work, brand credibility, and customer trust. For clients, this builds confidence that the process is necessary and valuable.

Set Realistic Expectations

No migration is risk-free. Be honest about possible short-term drops in rankings or design inconsistencies. What matters is showing a clear plan to recover quickly. Under-promising and over-delivering is far safer than creating false expectations.

Bottom line: when talking to CEOs or clients, drop the technical vocabulary and focus on outcomes. If they understand migration in terms of revenue, risk, and opportunity, they are far more likely to support the process and give it the resources it needs.

Strategies to Minimize Migration Problems

While migration challenges are real, they are not unavoidable. With careful planning, testing, and the right tools, most risks can be minimized. The key is treating migration as a structured project, not a quick technical task.

Start with a Full Audit

Before touching the new platform, audit the current website. Crawl all URLs with tools like Screaming Frog or Sitebulb, collect metadata, and back up media files. Document every page, redirect, and integration. This inventory will become your migration blueprint.

Use a Staging Environment

Never migrate directly to a live domain. Build the new site in a staging environment where you can test design, content, and functionality without risk. Only launch after thorough checks, ensuring redirects, forms, and tracking scripts work correctly.

Map Redirects Carefully

Create a one-to-one redirect plan for every old URL. Use 301 redirects to preserve link equity. Avoid redirect chains or sending multiple pages to a single destination. This keeps search engines confident that your new site is simply an improved version of the old one.

Test SEO and Analytics Early

Submit a test sitemap to Google Search Console before launch. Verify that analytics tags and goal tracking work as expected. Testing these elements early prevents weeks of lost data or inaccurate reporting.

Communicate Across Teams

Involve SEO specialists, designers, developers, and marketing managers from the start. Migration touches every discipline, and silos often cause the biggest mistakes. Aligning everyone on risks and responsibilities reduces surprises.

Key takeaway: migration success depends less on tools and more on preparation. A structured approach with audits, staging, and cross-team collaboration dramatically reduces the chances of costly mistakes.

When Should You Avoid Migration Altogether?

Not every website should be migrated. In some cases, the risks and costs outweigh the potential benefits, and staying on your current platform is the smarter move.

When Costs Exceed Value

If the main reason for migration is “just to try WordPress” or “because a competitor uses it,” think twice. A full rebuild can cost thousands in development and design, plus ongoing hosting and maintenance fees. Unless the new platform delivers clear long-term advantages — such as scalability, integrations, or custom features — the investment may not pay off.

When SEO Risk Is Too High

Websites with large backlink profiles or heavy reliance on organic traffic should approach migration cautiously. Even with careful planning, ranking fluctuations are likely. If your site depends almost entirely on SEO for revenue, the short-term dip may create unacceptable losses.

When Alternatives Exist

Sometimes the issues that trigger migration — like outdated templates or missing features — can be solved without leaving the current platform. SaaS builders often release new features or third-party add-ons that meet business needs without the risk of starting over.

Bottom line: migration should never be done “just because.” If the expected business value is unclear or the risks are disproportionate, it’s wiser to optimize the existing platform rather than rebuild from scratch.

Expert Advice from Paul Viatkin

From my experience working on dozens of website migrations, the majority of failures come from underestimating structure and SEO. Businesses often assume that as long as the content “moves over,” everything else will follow. In reality, about 80% of migration issues I’ve seen were caused not by design errors but by broken redirects, missing metadata, and poorly mapped site structures.

My strongest advice is to treat migration as a business continuity project, not just a design refresh. Before touching a new platform, build a complete map of your existing website — every page, every redirect, every integration. This becomes your safety net. Without it, you’re migrating blindly.

I also recommend involving both marketing and technical teams early. Too often, developers launch a migrated site without SEO oversight, or marketers expect design perfection without understanding technical limits. Migration succeeds when both sides collaborate from the start.

Finally, don’t rush. The fastest migrations are usually the most expensive in the long run, as you end up fixing mistakes afterward. A staged approach with audits, testing, and phased rollouts always delivers better results than a quick, “big bang” switch.

In short: the best migrations are invisible to end users and search engines. If no one notices the move, you’ve done it right.

Conclusion: Seeing the Full Picture of Migration

Website migration is rarely just a technical task. It is a business-critical operation that touches SEO, design, content, and customer trust all at once. Moving from SaaS builders to CMS platforms promises flexibility and long-term growth, but the process is full of hidden pitfalls. Broken redirects, missing metadata, lost media files, or inconsistent branding can turn a well-intentioned project into months of recovery work.

The key lesson is preparation. A detailed audit, clear redirect mapping, staging environments, and strong cross-team collaboration reduce most of the risks. Just as important is communication: executives and clients must understand that migration is not about switching tools but about protecting the digital asset that drives revenue and reputation.

Handled poorly, migration can cost money, rankings, and trust. Handled well, it becomes an invisible transition that positions your business for future success.

As someone who has managed migrations across multiple platforms, I can say with confidence: the smoothest projects are the ones where risks are anticipated, resources are aligned, and no step is rushed. Migration should always be treated as a strategic investment — because that’s exactly what it is.