Why can an ERP system integration be so complicated?

Many businesses assume that integrating an ERP system with their website or other software is a straightforward process. However, ERP integration involves deep technical expertise, strategic planning, and often custom development to ensure seamless connectivity between systems.

In this article, we break down the complexities of ERP integration, highlight key challenges businesses face, and explore available solutions — including plugins, automation tools, and custom integrations. We’ll also explain how HARMONiQ’s flexibility and Logiq’s expertise simplify this process.

6 complexities of ERP integration

ERP integration is a powerful way to streamline business processes but it can be a complex task with significant challenges. From data inconsistencies to system compatibility, here are six common challenges faced during the integration process.

1. Compatibility

ERP systems are designed to connect with other software solutions, including CRMs, inventory management systems, and websites. However, compatibility is a common hurdle.

Every system has unique capabilities and limitations, some legacy systems use outdated authentication methods that don’t support modern API-based integrations, and middleware solutions are sometimes required to bridge compatibility gaps.

At Logiq Group, we leverage HARMONiQ’s extensive integration capabilities to ensure smooth connectivity with HubSpot and other platforms.

2. Data complexities

Businesses have vast amounts of data, often stored in various formats and systems. Determining the "single source of truth" is critical to maintaining data integrity when integrating multiple business systems together.

Each system can have different names and data types for what is essentially the same data - one of the key challenges in any integration is mapping data between systems to avoid any data loss or corruption.

Another key challenge is managing data update frequency. Some systems update data in real-time, ensuring instant synchronisation across platforms, while others refresh information at scheduled intervals - daily, hourly, or on demand. The chosen frequency impacts operational efficiency, reporting accuracy, and system performance. If an ERP system integrates with platforms that operate on different update schedules, discrepancies can arise, leading to outdated or conflicting data. This can also make it more difficult to manage any duplicate records that might be created between systems.

3. Scalability

As businesses grow, ERP integrations must handle increasing data volumes, users, and transactions. Poorly designed integrations can lead to performance issues, system slowdowns, and costly infrastructure upgrades. Ensuring integrations can scale alongside business needs is critical for long-term efficiency.

4. Security

ERP systems handle sensitive data, including financial records and customer information. Integrating multiple platforms increases security risks such as data breaches and unauthorised access. Businesses must implement:

• Secure data transfer protocols (e.g., encryption, SSL/TLS).
• Role-based access controls to prevent unauthorised data exposure.
• Continuous monitoring for vulnerabilities in integrated systems.

5. Customisation

ERP integrations often require custom features to align with unique business needs. However, custom-built integrations can be difficult to troubleshoot and maintain.

In some cases, integrating an ERP system with a website, for example, requires a complete website overhaul. This is particularly true when the website is outdated and lacks the necessary API endpoints for ERP communication.

Customisation also requires in-depth knowledge of both the ERP system and the business processes. This necessitates a close relationship between the business and the ERP provider. 

6. Testing and debugging

ERP integrations involve multiple systems interacting in real time. This makes testing critical to ensure:

• Data flows correctly between platforms without errors.
• Third-party integrations and customisations function as expected.
• Performance remains stable under real-world conditions.

Debugging issues can be complex since errors often originate from multiple sources, requiring deep technical expertise to diagnose and resolve.

Common ERP integration methods

Modern ERP systems like HARMONiQ use various integration methods to connect with other platforms. The most common methods include:

• API-based integrations – web services allow real-time data synchronisation, ensuring instant updates and automation across systems.
• File-based transfers – older systems may rely on scheduled CSV or FTP file exchanges to transfer data at set intervals or triggered when files change.
• Third-party automation tools – platforms like Zapier, Make, Power Automate, and RabbitMQ provide flexible integration options, automating workflows between ERP systems and other applications.

Common integration types 

ERP systems integrate with a wide range of business tools and platforms, including:

• Websites – connecting e-commerce or company websites for seamless order processing and inventory updates.
• External CRMs – ensuring customer data flows between ERP and customer relationship management tools like HubSpot.
• Warehouse Management Systems – automating stock levels, logistics, and inventory tracking.
• Marketing Automation – syncing data with platforms like Mailchimp to enhance customer engagement.
• Supply Chain Systems (EDI & Punchout) – facilitating direct integration with customer or supplier systems for procurement efficiency.
• Business Intelligence & Reporting – connecting with analytics tools like Power BI and Tableau for real-time data insights.

By leveraging the right integration method, businesses can streamline operations, reduce manual effort, and enhance data accuracy across all critical systems.

ERP implementation services

At Logiq Group, we specialise in end-to-end ERP implementation. From the initial discovery phase to ongoing training and support, we’ll make sure your new system is seamless, easy to use, and optimised for your operations. 

Get an estimate with our Cost Calculator 

Choosing the right ERP system is a big decision, and understanding the investment is key. Our Cost Calculator helps us to understand your needs, accounting for your company structure and scale, operations and warehouse management, implementation resources, and integration requirements. 

In a few minutes of completing the quiz, you’ll get a personalised cost estimate tailored to your needs. Try it now by clicking below: