Top 10 Cons & Disadvantages of Shopify

by Peter Kanai · March 2, 2025

Shopify has emerged as one of the most influential e-commerce platforms in the world. It provides entrepreneurs with an easy-to-use store builder, allowing anyone to launch an online shop without needing extensive technical skills. Over the years, Shopify’s ecosystem has grown to serve millions of businesses globally, from small home-based shops to major international brands. Its success is rooted in offering a turnkey solution – hosting, payment processing, themes, and apps – that simplifies the complexities of online retail.

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However, no platform is perfect, and Shopify is no exception. While it excels in ease of use and scalability, users have discovered certain limitations and downsides through their experience. These drawbacks range from financial costs to technical constraints that can impact a store’s operation and growth. For anyone considering Shopify, it’s important to look beyond the hype and examine the platform’s disadvantages alongside its benefits.

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In the following sections, we will delve into the top 10 cons of using Shopify. Understanding these issues is essential for making an informed decision about whether Shopify fits your needs.

1. High Costs and No Free Plan

A major drawback of Shopify is its pricing model. Unlike some competitors that offer free plans or open-source solutions, Shopify requires a monthly subscription after a brief trial period. This means merchants must budget for ongoing costs from the outset, which can be challenging for startups or small businesses on tight budgets.

Monthly plans range from $32 to $399, offering different feature tiers for various business sizes
There is no permanent free tier, only a 3-day free trial and a temporary $1 first month for new users
Credit card processing fees on each sale still apply, adding to the costs.

Real-Life Example: A small boutique owner launched her store using Shopify’s trial, but after the first month she began paying the standard $32 per month for the Basic plan. This recurring cost meant she needed to ensure consistent sales just to cover the platform fees and justify staying on Shopify.

Solution: To mitigate high costs, merchants can start with the most basic plan and only upgrade when their revenue grows sufficiently. Careful budgeting and taking advantage of annual plan discounts (which reduce monthly fees by about 25%) can help manage the expense.

2. Transaction Fees and Hidden Expenses

Beyond the base subscription, Shopify can incur various hidden expenses. Users often face additional transaction fees if they opt for payment gateways other than Shopify’s own, and these charges can eat into profit margins. Furthermore, many advanced features require paid apps or add-ons, meaning the true cost of running a Shopify store can be higher than expected.

Shopify charges up to a 2% fee on transactions if not using Shopify Payments, on top of regular credit card processing fees.
Many advanced features require third-party apps with their own monthly fees.
One-time expenses (like a premium theme or domain name) also add to your overall costs.

Real-Life Example: A merchant in a country where Shopify Payments isn’t available might use PayPal or another gateway and find that Shopify takes a 2% cut of each sale for that choice. Combined with paying $15/month for a couple of necessary apps, the store owner’s monthly bill ends up significantly higher than the base plan price.

Solution: To handle these extra fees, store owners can try to use Shopify Payments where possible to avoid transaction surcharges or seek gateways with lower fees. It’s also wise to judiciously select only the apps that add clear value to your business and periodically trim unnecessary subscriptions to keep costs manageable.

3. Limited Theme Options

Shopify offers many store themes, but the selection of free designs is very limited. With only around 13 free designs available, many Shopify stores end up looking similar unless owners invest in a paid theme or custom design. This can make it challenging for a brand to stand out visually without spending extra money on design.

Shopify provides just 13 free themes (out of hundreds of total themes), giving budget-conscious users few choices.
Premium themes can cost $150–$500 each, adding to startup expenses if you want a specific look.
Customization of themes often requires editing Liquid code or hiring a developer if you need a truly unique layout or features.

Real-Life Example: An online fashion boutique owner found that the default free theme made her site look generic and similar to other shops. She ended up purchasing a $300 premium theme to achieve the elegant, unique look she envisioned for her brand.

Solution: A cost-conscious workaround is to start with a free theme and customize it within its limits by changing colors, images, and fonts to reflect your brand. Alternatively, merchants can look for third-party theme discounts or use page builder apps to enhance a free theme’s design, delaying the need for a pricey theme upgrade.

4. App Dependency for Advanced Features

Out-of-the-box, Shopify provides core eCommerce functions, but many advanced features are missing and must be added via apps. Whether it’s adding customer reviews, loyalty programs, or complex shipping rules, merchants often end up installing multiple apps to gain needed functionality. This dependency on apps can increase costs and sometimes introduce technical issues if apps conflict or slow down the site.

Common needs like marketing pop-ups, product reviews, or wishlist functionality are not built-in and require separate apps.
Each app typically charges its own monthly fee or has usage limits, which can significantly increase the overall cost of running the store.
Too many apps can bloat your website, potentially affecting loading speed and user experience.

Real-Life Example: A Shopify electronics store owner installed five different apps (for reviews, live chat, upselling, email pop-ups, and SEO). While these apps extended his store’s capabilities, they also collectively added about $50 to his monthly costs and made the site slightly slower to load.

Solution: Store owners should be selective with apps: install only those that are truly necessary and look for apps that serve multiple functions to reduce bloat. Periodically auditing app usage and removing redundant or unused apps will help keep your store streamlined and costs under control.

5. Restricted Customization and Flexibility

Another drawback is that certain aspects of a Shopify store are not fully customizable unless you’re on the highest plan or willing to delve into code. The checkout page’s design and functionality cannot be changed on standard plans, limiting how you can tailor the final steps of the purchase process. Additionally, Shopify uses its own templating language, Liquid, which has a learning curve and can pose challenges for those unfamiliar with it.

Shopify does not allow customization of the checkout on regular plans, meaning you can’t add custom fields or redesign the checkout flow without Shopify Plus.
Implementing certain features (like post-purchase upsells or custom user account pages) may require Liquid code edits or apps, since there’s no direct access to backend code beyond the theme layer.
Unlike open-source platforms, you cannot change core functionalities; you are limited to what Shopify provides and what apps can do, which can frustrate businesses with unique requirements.

Real-Life Example: A subscription-box business wanted to add a questionnaire in the checkout to personalize orders, but found that impossible on their Shopify Basic plan. They had to settle for emailing customers after purchase, as full checkout customization wasn’t accessible without upgrading or using a costly third-party solution.

Solution: To work around Shopify’s customization limits, merchants can use apps that inject certain functionalities (for example, upsell or survey apps that integrate around the checkout process). Those with specific needs might consider alternative platforms or plan for a Shopify Plus upgrade if a custom checkout or deeper code access becomes crucial for their business.

6. Platform Lock-In and Data Migration

Once a store is built on Shopify, migrating to another platform can be complicated. Shopify’s system is proprietary, which means your store’s design and content are not easily transferable to other eCommerce platforms. Exporting basic data (like products and customers) is possible, but rebuilding the full site elsewhere often requires significant effort or technical assistance.

Shopify uses a unique template structure and apps that don’t have direct equivalents on other platforms, making a move labor-intensive.
Merchants may feel “locked in” because switching platforms means potentially losing theme customizations, app functionalities, and possibly SEO rankings during the transition.
Unlike open platforms (e.g., WooCommerce on WordPress), you cannot simply take your Shopify site and host it elsewhere – you’d essentially have to start anew on a different system.

Real-Life Example: A growing retailer decided to migrate from Shopify to a self-hosted solution to save costs, but they discovered that none of their Shopify theme or app customizations could be exported. They had to hire a developer to recreate their site’s look and features on the new platform, causing downtime and added expenses.

Solution: To minimize lock-in pain, it’s wise to regularly back up your store data (products, customer lists) and keep copies of site content. If you anticipate possibly outgrowing Shopify, consider a more flexible platform early on or use a headless commerce approach where your front-end is separate, which can make future migrations easier.

7. Limited Blogging and Content Features

Shopify includes a basic blogging tool, but it’s not as robust as dedicated content management systems. For merchants who rely heavily on content marketing or SEO through blog posts, Shopify’s blogging interface may feel limiting – for instance, it lacks advanced categorization and plugin options that platforms like WordPress offer. Managing a content-rich site on Shopify can become cumbersome, especially if you need features like content versioning or sophisticated editorial workflows.

Shopify’s blog supports tagging but does not natively support multiple categories or content hierarchies, limiting how you organize posts.
Features like scheduled posts, SEO plugins, or advanced media management are either basic or require additional apps to achieve similar functionality.
Heavy content sites (e.g., news sections or lookbooks) might find Shopify’s content editor simplistic, potentially necessitating an external blogging platform for full flexibility.

Real-Life Example: A health and wellness store attempted to run an extensive blog with recipes and articles on Shopify. They eventually faced difficulties with organizing content and adding custom features, leading them to start a separate WordPress blog linked to their Shopify store.

Solution: If content is a big part of your strategy, you can integrate Shopify with a more powerful blogging platform or use apps that extend Shopify’s blogging capabilities. Another approach is to keep the main store on Shopify but manage content-heavy sections on a different system (such as a subdomain or headless CMS) that feeds into your site.

8. No Built-In Email Hosting

Unlike some all-in-one web hosting services, Shopify does not include email hosting for your custom domain. This means if your store domain is yourstore.com, Shopify won’t provide you with an @yourstore.com email service. Merchants have to set up email addresses through third-party providers (like Google Workspace or others), which is an extra step and expense in getting the business running.

Shopify provides domain purchasing but not email accounts, so you’ll need to use an external email host for addresses like info@yourstore.com.
This adds an additional cost (for example, Google Workspace starts at around $6 per user per month) and requires technical setup of MX records on your domain.
New store owners may find it inconvenient to manage the store and the email on different platforms, rather than in a single unified solution.

Real-Life Example: After launching their Shopify store, a small business owner realized they couldn’t create a business email through Shopify itself. They had to sign up for a separate email hosting service to get a professional email address, incurring an extra monthly fee.

Solution: The solution is to use a reputable third-party email hosting service alongside Shopify. Many domain registrars offer free email forwarding, or you can use services like Zoho Mail (which has a free tier) or Google Workspace to handle your store’s emails and maintain a professional image to customers.

9. Limited Customer Support Channels

Customer support from Shopify is available 24/7, but the channels are somewhat limited depending on your plan. While you can reach out via live chat or email at any time, phone support is notably missing for most users unless you’re on a higher-tier plan. This can be frustrating in urgent situations when speaking directly to a support agent could resolve issues faster.

Shopify’s standard support is through live chat and an online help center; telephone support is only offered to Shopify Plus or certain higher-tier customers.
Response times on chat can vary, and complex technical issues might get escalated to email support, which takes longer to resolve.
Merchants who prefer real-time voice support may feel underserved, especially during critical issues that impact sales.

Real-Life Example: A store owner experienced a payment glitch during a weekend sale and wanted immediate help. Without phone support on her plan, she had to rely on live chat, spending valuable time explaining the issue and waiting for resolution while potential orders were delayed.

Solution: To overcome support limitations, merchants can proactively use Shopify’s help center and community forums to troubleshoot common problems. It’s also helpful to build a relationship with a Shopify Expert or agency for complex issues, and if your business demands high-touch support, consider upgrading your plan or using a platform known for dedicated account managers.

10. Shopify Payments Not Available Everywhere

Shopify’s proprietary payment gateway, Shopify Payments, is a convenient feature that reduces transaction fees, but it’s not available in all countries. Businesses operating in unsupported regions cannot use Shopify Payments and must rely on third-party payment gateways instead. As a result, they often face additional transaction fees and potentially a more complicated setup with external providers.

Shopify Payments is limited to certain countries (mostly North America, Europe, and a few Asia-Pacific regions), leaving out many markets.
If your country isn’t supported, you’ll have to use alternatives like PayPal or local gateways and pay Shopify’s extra transaction fee on each sale.
Lack of Shopify Payments also means missing out on features like integrated payouts and a streamlined checkout experience that Shopify’s native system provides.

Real-Life Example: A merchant in Brazil (where Shopify Payments is unavailable) must connect a third-party payment processor for credit card payments. This not only adds a layer of complexity in managing payouts and technical integration, but also means Shopify charges additional fees on each sale because he isn’t using their in-house payment system.

Solution: A potential solution is to advocate for Shopify to expand Shopify Payments to more countries, but in the meantime, affected merchants should compare third-party gateway options to find the most cost-effective one. Additionally, structuring pricing to account for the extra fees or offering alternative payment methods (like cash on delivery or bank transfers) for local customers can help mitigate the impact of not having Shopify Payments.

How Could These Disadvantages Be Overcome Globally?

The challenges posed by Shopify’s shortcomings are not insurmountable, and many can be addressed on a global scale through collective effort and platform improvements. Both Shopify as a company and the wider eCommerce community are continually developing solutions to minimize these pain points. Overcoming these disadvantages globally involves a combination of platform changes, third-party innovations, and knowledge sharing. For example, Shopify can introduce new features or policies while developers worldwide create apps and tools to fill the gaps. By recognizing these issues, the eCommerce industry can push for changes that benefit merchants everywhere.

More Inclusive Pricing Models: Shopify could implement region-specific pricing or introduce a limited free plan worldwide to support entrepreneurs in emerging markets.
Expanded Payment Support: By rolling out Shopify Payments to more countries and supporting a wider range of local payment methods, the platform can reduce transaction fee burdens globally.
Improved Customization Tools: Ongoing development of the platform (and new features) could give merchants more built-in customization options, decreasing reliance on apps and custom code.
Data Portability Standards: Industry-wide efforts (possibly led by Shopify) to standardize eCommerce data export/import would make it easier for merchants to migrate stores or integrate multiple platforms without losing information.
Global Education and Support: Creating more accessible learning resources, multilingual support, and strong community forums can empower store owners around the world to overcome challenges by sharing solutions and best practices.

Top 5 Best Shopify Marketing Agencies

To further help Shopify merchants succeed, a number of specialized marketing agencies have emerged globally. These agencies focus on Shopify and eCommerce, offering services from store design to digital marketing campaigns that drive traffic and sales. Partnering with a top Shopify marketing agency can help store owners overcome some platform limitations by optimizing the store and implementing advanced strategies. They bring expertise in areas like SEO, conversion rate optimization, and advertising tailored specifically for Shopify stores. Below are five of the best Shopify-focused marketing agencies known for helping merchants grow:

The Charles – A New York-based Shopify Plus partner agency renowned for creating high-end, custom online shopping experiences and comprehensive marketing campaigns for enterprise clients.
Cake Agency – A UK-founded agency (“by retailers for retailers”) that offers full-service Shopify design, development, and innovative growth strategies to rapidly scale eCommerce brands.
Top Growth Marketing – A Shopify-specialized marketing firm led by industry experts, focusing on paid advertising, conversion rate optimization, and strategic coaching to help stores achieve explosive growth.
Stryde – A digital marketing agency that works closely with Shopify merchants, providing SEO, social media advertising, and email marketing services to drive targeted traffic and increase sales.
Lamb Agency – An Australian Shopify expert agency known for optimizing store design and user experience; they’ve helped clients achieve significant conversion rate improvements through tailored eCommerce strategies.

What is Shopify?

Shopify is a subscription-based online commerce platform that allows individuals and businesses to create and run their own online stores. Founded in 2006, it has grown into one of the leading eCommerce solutions globally. The platform handles the technical infrastructure, so users can focus on products and sales rather than web hosting or coding. Shopify offers an intuitive interface and a suite of built-in tools that cover most needs of an online retailer. From small hobbyists to major brands like Kylie Cosmetics, millions have used Shopify to power their eCommerce ventures.

Easy Store Setup: Shopify provides user-friendly store templates and a drag-and-drop editor, enabling quick setup without needing to code.
Secure Hosting: All Shopify stores are hosted on Shopify’s servers with SSL security and reliable uptime, so merchants don’t worry about server management.
Built-in Payments: It includes Shopify Payments (in supported countries) and integrates with numerous gateways, making it simple to accept credit cards and other payments.
App Ecosystem: Shopify’s App Store offers thousands of plugins for extending functionality – from SEO tools and email marketing to dropshipping integrations and more.
Multi-Channel Selling: Merchants can sell not only on their Shopify website but also connect to marketplaces like Amazon, social media platforms, and even in-person with Shopify’s POS system.

Real-Life Example: For example, a local coffee roaster used Shopify to set up an online store to sell beans and merchandise, handling payments and inventory with ease. On the other end of the spectrum, Kylie Cosmetics famously ran on Shopify, demonstrating the platform’s capability to handle huge traffic and sales volumes during product launches.

Videos about Shopify

Videos can be an excellent resource for learning more about Shopify, offering visual step-by-step guidance and unbiased reviews. Whether you prefer official tutorials or community-made content, there’s a wealth of information on platforms like YouTube to help you master Shopify.

Conclusion

Shopify’s position as a leading eCommerce platform comes with undeniable strengths, but it is equally important to acknowledge its weaknesses. By understanding the cons discussed above, merchants can make more informed decisions and implement strategies to mitigate common issues. Many successful businesses still thrive on Shopify by leveraging workarounds and staying adaptable. Shopify has also responded to feedback by rolling out features to address some of these drawbacks.

Still, merchants should remain vigilant and adaptive, taking advantage of community resources and professional expertise when needed. Ultimately, the key takeaway is that no platform is perfect; the best approach is to weigh Shopify’s pros against its cons in the context of your specific business needs and to be proactive in overcoming any hurdles.