Shopify sellers shouldn’t just stick to one store; instead, you can build multiple Shopify stores to grow the diversity of your brand. However, managing multiple stores on Shopify comes with many challenges.

We don’t want you to feel that way! You shouldn’t stay back from expanding your business.

In this blog, we will highlight the common multiple Shopify store issues and how you can overcome them in the right possible way. 

Multiple Shopify Stores Issues

Creating multiple stores on Shopify can be easy, but managing them correctly is very difficult.

Every single thing comes with some flaws, and Shopify is on the same platform; although it provides you with many features, but it too has some drawbacks.

You should be familiar with the issues that you will be facing while having multiple stores on Shopify, and remember that there are possible solutions for each one.

Top Common issues of Shopify stores & their solutions

These are some of the common Shopify issues that you may face:

  • ERP integration
  • Less increase in sales
  • Getting products on store
  • Marketing management
  • Difficulty in finding customers
  • Managing Analytics
  • Multi-channel selling management

1. ERP Integration

ERP (Enterprise Resource Planning) refers to the system software that e-commerce persons use to manage day-to-day activities. It combines multiple business processes and enables the data flow between them.

To build an online store and sell products, you must integrate your business ERP with the Shopify store to automate the multiple business processes and manage day-to-day activities.

ERP entails processing orders, shipping, billing, and managing the supply chain issues for Shopify users. 

Indications that can show you need ERP integration may include the following;

  • It has lots of suppliers to manage
  • Late shipping of the products
  • Wrong shipping due to high volume of products
  • Low employee productivity because of doing the tasks manually

ERP integrations are often complex, time-consuming, and require expertise.

Most Shopify users are not familiar with technical things, thus integration is a complex venture, and it comes with multiple challenges to implement successfully.


It would be helpful if you could determine how your ERP system is receiving and delivering the data, and how it communicates with other systems.

If your system faces trouble connecting to other systems, then the connection between Shopify and these systems is limited.

You should consider a cloud-based ERP system having an open and well-documented API because it’s easy and simple to integrate.

It is generally effortless to use, and an affordable option for small to medium-sized businesses. Cloud-based ERP systems offer reduced IT infrastructure costs and lower upfront investment.

2. Less increase in sales

This is the most common issue of Shopify’s multiple stores, a huge amount of traffic does not mean a large number of sales.

Getting the right number of customers for your product is the main issue encountered by many sellers; it is always a challenge for them to convert prospects into customers.


You should provide your products to the customers who actually need them. You must be familiar with how to manage the scenarios to increase the sales.

If you want to build trust with your customers, you can design multiple ad campaigns, provide a sure-shot cash-back guarantee, share customer feedback or experience, and so more.

Are you spending too much time managing your multiple Shopify stores?

Apimio PIM can help you save time, streamline your workflow, and grow seamlessly.

3. Getting products on store

Importing your products to Shopify stores is one of the issues. You can easily import your products by using the CSV file, but if there is an error, the whole process can fail.

If it fails in the mid-process, then you will only be left with the option to import the products manually one by one.

This is feasible if you have fewer products, but if you are dealing with more than a thousand products, then it can become a major issue for your business.

You will have to update the Attributes, Categories, and Images repeatedly with every product. For instance, imagine uploading thousands of products in a short period.


Inventory management is the answer to this whole issue. As a vendor dealing with Shopify multiple stores, you must implement the best inventory management system in real time.

Having the right and accurate data on hand can save the selling from being risky. Lacking such data may affect the various operations of businesses irrespective of how you look at it in the long run. 

4. Marketing Management

Managing multiple marketplaces simultaneously is very difficult for persons dealing with businesses, even if you are a small business owner.

Being a store owner, especially when you are new on Shopify, it can become challenging for you to manage multiple things like the status of inventory, product management, sales, shipping, checking SKUs, and so more.

It can become even worse when your store demands optimum attention 24\7 every day of the week.


To overcome this issue, Shopify has worked with a wide range of apps to help you operate your business as smoothly as possible. Some examples of these apps are;

  • CedCommerce
  • Omnisend It allows the customers to leave reviews for you that you can review automatically.

CedCommerce: This app helps you share the load of getting inventory status, SKUs, shipping, and order management for all the marketplaces.

Omnisend: It allows campaign automation for emails and SMS marketing. It is helpful for large-scale campaigns.

5. Difficulty in finding customers

Beginners in the e-commerce industry, for the first time, are likely to face this issue of attracting customers to their items.

For the first time, it is difficult for the newbies to drive traffic to each of their products because the e-commerce business is different from traditional marketing. 


Being aware of the pros and cons of Shopify can help you solve this issue.

Make sure you are familiar with the advantages and disadvantages of other e-commerce platforms, so you can come up with a proper strategy to attract more customers.

Other ways may include promoting your business through advertisements and campaigns.

Collaborate with social media influencers, work with them, and pay for shoutouts. And lastly, work on the optimization of your store for a better engagement of customers. 

Looking for ways to improve your SEO and increase sales?

Schedule a demo with our SEO Specialist and get a personalized strategy for success.

6. Managing Analytics

One of the most overlooked components for your e-commerce business is the analytics report for your Shopify multi-store.

This shows you how well your Shopify multi-stores are working and where you need to improve. Analytics tools sometimes report the data very slowly, and this speed can become annoying sometimes.

If there are no well-defined actionable insights, it will be tough to implement modifications in your stores to optimize the performance.

Not giving attention to your store analytics is undoubtedly a mistake that can destroy your Shopify store, but another worst issue is not knowing where to start with the tons of statistics to look at. 


As the business grows, the requirement for information analysis also grows with time. In the e-commerce world, analysis plays an important role.

Besides predictive analysis, store owners need real-time data and some insights to customize their inventory, marketing, and more to enhance their sales.

Shopify users must use an analytics app that can help them to run their business smoothly and offers real-time predictive analytics. 

7. Multi-channel selling management

Customers are shopping from more than one place than ever, in the time of desktops and mobile devices. Without any doubt, multi-channel selling will shape the future of e-commerce.

Having said that, the advantages of multichannel selling are just the tip of the iceberg. The actual management of multi-channel may be extremely tricky and demanding.

Therefore, moving towards the omnichannel retailing strategy is essential to not lag behind competitors.

Omnichannel and multichannel are two different aspects, apart from the fact that they both need selling over numerous sales channels.

Omnichannel merges all the sale channels into a single system, and multichannel handles all the communication channels independently. 


To overcome these problems, you need to identify the essential channel to focus on. Along with Shopify, you should think about linking your Shopify multi-stores to other marketplaces like Amazon and Etsy. 

Besides that, you should also centralize your data, inventory, and orders into a single system to easily manage all of the aspects of your Shopify stores consistently.

Moreover, make sure that all of your touchpoints need to be unified, such as brand messages and pricing.


We have incorporated the common issues faced by many e-commerce managers having multiple stores on Shopify and tried to mention all the possible solutions to fix them.

Every seller must deal with many of these problems to overcome the processes.

On the bright side, all the problems can be fixed by simply implementing the possible solutions we have provided you with.

What to do next?

  • Want to know how you can manage multiple Shopify stores? Head on to our blog.
  • Create an account now and transform your business. Sign-up here.
  • Contact our support if you have any questions or issues.

Frequently Asked Questions

1. Why do so many Shopify stores fail?

There can be so many reasons for this, but the most common are; not having a niche, not understanding e-commerce, not having enough traffic, and not making enough sales.

2. Why is Shopify the best?

Shopify has its own customizable features and customer support 24/7. It is secure, reliable, and also mobile-ready. It offers the POS (point of sale), which makes it highly possible for you to be able to process orders and take payments in person.

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