Shopify has emerged as a leading ecommerce solution for B2B companies in recent years, with more and more choosing it when replatforming. This has resulted in huge growth in Shopify’s B2B gross merchandising value, which grew by 96% in 2025 (Digital Commerce 360).
With strong standing in the B2C market, Shopify has successfully adapted to the complexities of B2B sales processes and is able to provide the features, sophisticated account management and complex integrations that the market requires.
Shopify has also achieved a reputation as an ecommerce platform that is easy to set up and manage in-house by merchants. This is thanks to it operating as a SaaS (software as a service) platform, its user friendly interface and the vast array of plugin feature apps that are available.
The above has led B2B merchants to question whether replatforming to Shopify is something they can manage themselves, or whether they require the support of a Shopify B2B specialist agency to help them to make it a success.
In this article I will share my insights on this area as the head of B2B ecommerce agency Fluid Commerce so that business leaders can decide whether they have the capabilities to go it alone, or whether having input from a Shopify specialist agency is necessary.
What’s actually involved in launching a Shopify B2B store?
The first, and most critical, aspect to get right is to clearly define the requirements of the company’s online store and self-service customer portal and the workflows that will need to be followed.
This will include setting out the account management roles and users, custom pricing and catalogues, customer requirements for features such as stock level checks, track orders and request a quote.
The next task will be to select the correct Shopify plan, with enterprise level companies, high volume merchants and fast-growing B2B retailers overwhelmingly utilising the Shopify Plus plan. One example is Fluid Commerce client and leading jewellery wholesale company Gecko which recently replatformed to Shopify Plus. You can read more about that Shopify Plus project here.
The native B2B features aligned with the Shopify Plan then need to be configured correctly, which can be relatively straightforward, and possible to be completed by an in-house ecommerce team that has moderate technical expertise.
Following this, careful attention needs to be given to integrating the business critical systems such as ERP (enterprise resource planning) and OMS (order management system) systems, among many others. Integrations with Shopify Plus vary in complexity, with some that can be done with an iPaas platform such as Patchworks or Shopify connectors for systems such as NetSuite and Microsoft Dynamics 365, while others require significant planning and custom development.
Product data needs to be migrated to the new Shopify platform without any loss to its integrity. This is probably one of the most challenging aspects of any B2B platform migration project due to the complexity of the data and the thousands of SKUs that are utilised.
Another crucial, and sometimes overlooked, aspect of launching a B2B ecommerce store on a new platform, including Shopify, is the requirement for technical SEO and tracking to be put in place to ensure search engine visibility.
Finally end-to-end testing of the site needs to be undertaken to ensure the user experience and ecommerce journey of customers is operating perfectly.The testing should cover every stage of the buying journey, from the customer landing on the site, placing the order, through to despatch and account management, paying specific attention to the integrations and expected outcomes.
Can B2B merchants launch on Shopify themselves?
For some smaller, B2B merchants, launching on, or migrating to, Shopify themselves without agency input is a viable option, but this will still depend on the specific requirements of their customers’ buying journey, the complexity of the integrations required and the internal resources available to them. Most B2B companies need the support of a Shopify B2B specialist agency to at least some degree to ensure they do not suffer an interruption to their business operations and an unfortunate loss of sales and revenue.
Smaller B2B companies that do decide to go it alone often start by utilising their internal ecommerce or digital teams for management of the process. The many Shopify user guides and tutorials that exist can mean that some internal teams, particularly those with prior experience of the Shopify platform, can feel empowered to manage the project themselves without any external support.
However, it is important to recognise the limitations of a DIY approach. Without a cohesive technical strategy and a team of agency experts responsible for the project’s success, projects can quickly become messy, cost businesses more money to sort the issues out and the loss of customers who may not stick around to wait for a website to become functional again.
The hidden challenges of DIY Shopify B2B builds
While Shopify is often perceived as easy to implement, B2B ecommerce introduces a layer of complexity that is not always immediately apparent.
One of the most common challenges is the gap between native platform features and the actual real life requirements of a company. Although Shopify’s B2B functionality is robust, many merchants require bespoke workflows, approval processes or pricing structures that extend beyond standard capabilities.
Integrations can represent a significant area of complexity that needs a careful approach. Connecting Shopify with some ERP, OMS, CRM or PIM systems is not always straightforward, particularly with older legacy systems. This necessitates careful planning around data flows, synchronisation and error handling. Without experience in this area, integrations can become difficult and potentially cause long-term problems.
As the business grows, scalability can become another concern. What works for a smaller operation may not hold up under increased order volumes, expanded product catalogues or international expansion.
There is also the risk of accumulating technical debt. Quick fixes, over-reliance on apps and poorly structured implementations can lead to the need for expensive rework further down the line.
Finally, time-to-market is often impacted. What initially appears to be a cost-saving exercise can result in delays, as internal teams balance the project alongside their existing responsibilities.
What a specialist Shopify B2B agency brings
Working with a specialist Shopify B2B agency introduces a level of expertise that can significantly reduce risk, improve outcomes and limit the need for revision work needing to be undertaken down the line.
For B2B ecommerce companies that need additional functionality not covered by Shopify’s native features, custom development expertise from a specialist agency is invaluable. This was something our client Gecko found made a positive impact on their Shopify Plus project.
Another key advantage is that specialist agencies have a deep understanding of Shopify’s B2B ecosystem, including its capabilities, limitations and the most effective ways to extend it. This enables agencies to design solutions that are both robust and aligned with best practices.
Specialist agencies also bring experience in handling complex B2B requirements, from multi-tier pricing and customer hierarchies to advanced ordering workflows and self-service portals.
From a technical perspective, they provide solution architecture and strategic planning, ensuring that all components of the platform work cohesively. This is particularly important when multiple systems and integrations are involved. At Fluid Commerce we have established processes and plans for how our clients’ projects will be handled from start to finish to ensure they run like clockwork. An internal ecommerce manager, who has numerous other responsibilities, will not be able to prepare for and manage every aspect of a new site launch to anywhere near the same degree.
Expertise in providing seamless integrations with existing business systems is another critical benefit of using a specialist agency. Agencies can design and implement reliable data migration strategies to ensure the process is seamless and they will have experience of performing this task successfully countless times before.
Ultimately, an agency’s focus is professional management of every stage of the launch or migration and while it may be tempting for some companies to try to handle the project in- house with existing staff, the costs associated with putting things right and loss of sales and revenue can stack up quickly.
How to decide what’s right for your business
Choosing the right approach ultimately comes down to a clear and honest assessment of your organisation’s capabilities and requirements.
This begins with evaluating your internal resources, including both technical expertise and available capacity to deliver the project effectively. If you employ in-house Shopify Plus developers, this is an entirely different scenario to handing a Shopify launch or migration project to an ecommerce or digital marketing manager.
It is also important to fully understand the complexity of your B2B requirements, from pricing and catalogues to integrations and customer workflows.
Balancing speed to launch against long-term scalability is another key consideration. While a quicker, lower-cost approach may be appealing, it is essential to consider whether it will support future growth and whether it will be cost-effective in the long-term.
How to choose the right Shopify B2B agency
For those that do decide to engage an agency, selecting the right partner is critical to success.
Proven experience and expertise with Shopify B2B projects should be a primary consideration, as this demonstrates an understanding of the platform’s nuances and challenges. The ability to handle integrations and complex builds is equally important.
Beyond technical capability, agencies should demonstrate strategic thinking, contributing not just to delivery but to the overall direction and success of the ecommerce solution for its long-term success. What established and proven processes do they already have in place to ensure nothing can go wrong and growth will happen quickly?
Transparency in their methods and a proactive approach to updating clients on the project’s progress are also advantageous so that companies can be reassured that their budget is being spent well.
Finally, be sure to carefully review relevant case studies and their measurable results, comparing them to your own business model to ensure their experience is fully inline with what you need.
Conclusion
Shopify has firmly established itself as a powerful platform for B2B ecommerce, offering a flexible and scalable foundation that is attractive to a wide range of business models.
While some smaller B2B merchants with simpler buying journeys can successfully launch independently, most will need the expertise of a specialist agency to ensure a successful launch and that there is no disruption to their sales and revenue.
Ultimately, the decision should be viewed not simply as a cost consideration, but as a strategic investment in the long-term success and scalability of your ecommerce operation.
Want to investigate what a specialist Shopify B2B agency can offer?
As a Shopify B2B specialist agency, Fluid Commerce is able to help companies to launch on or migrate to the platform with ease. To talk to us about how we can help your Shopify B2B project contact us here.
