Embedded vs. Integrated AP Automation: Which Solution Fits Your Team Best?

Embedded, integrated, or somewhere in between?

When it comes to AP automation, how your software is built can either streamline your processes or add unexpected complications.

If your team is juggling multiple logins, switching between screens, or managing disconnected tools, you’re likely facing more friction—and more chances for mistakes.

That’s why, whether you’re exploring new options or reassessing your current setup, it’s crucial to ask: Is this solution helping us work smarter, or making things harder?

In this article, we dive into the key differences between embedded and non-embedded (integrated) AP tools, what each means for day-to-day operations, and why an embedded solution could provide a smoother, safer experience.

What does “Embedded” really mean?

“Embedded” isn’t just a buzzword—it refers to a tool that’s built directly into your core system, functioning as a natural extension of your ERP. It’s not something bolted on or accessed separately—it’s just there, working in sync with everything else.

Think about how a fitness tracker records your heart rate, or how you can pay for something in an app without opening your banking app. Those seamless experiences are made possible by tight, behind-the-scenes integration. To the user, it just works.

Now let’s bring this back to AP automation.

Although “embedded” and “integrated” are often used interchangeably, they offer very different experiences.

Embedded AP Software:

• Fully lives inside your ERP
• One login, one interface
• Real-time data flow—no file uploads or tool-switching
• Built-in security through ERP role permissions
• Best for teams that want centralized control, clean workflows, and consistent governance

Non-Embedded (Integrated or Stand-Alone) AP Software:

• External platform that connects via APIs or file transfers
• Accessed through a separate portal
• Syncs data in batches, not in real time
• May offer specialized AP features
• Ideal for companies using multiple ERPs or looking for highly tailored functionality

Too Many Tools = Too Much Complexity

Many AP teams are still working across fragmented systems, leading to duplicate work, unnecessary steps, and increased chances for error.

Choosing the right solution isn’t just about ticking off features—it’s about finding a system that supports your daily workflow and long-term goals.

Embedded software often provides a cleaner experience: fewer tools, less switching, and more control.

If you're exploring better AP options, Mekorma offers embedded solutions for both Dynamics GP and Business Central.

• For BC, download Mekorma Payment Hub from AppSource and try it free for 30 days.
• For GP, get started here.

At the end of the day, AP automation should simplify, not complicate. The right tool empowers your team, reduces risk, and supports your organization’s financial success.

Comparing ROI: Embedded vs. Non-Embedded AP Automation

When Integrated Solutions Might Be the Better Fit

While embedded AP solutions offer a seamless user experience, they're not always the ideal choice for every organization. In certain cases, an external or integrated system may be the right call—especially if your needs extend beyond what embedded tools can offer.

Here are a few scenarios where non-embedded (integrated or stand-alone) solutions may make more sense:

• Your ERP doesn’t support embedded AP tools – An external solution can deliver automation without requiring an ERP switch.
• You need specialized or advanced features – Some stand-alone platforms offer robust functionality not yet available in embedded tools.
• Your team is already comfortable working across platforms – If dual-system workflows are already part of your routine, an integrated tool might not disrupt productivity.

That said, embedded solutions are often the fastest path to greater efficiency, improved controls, and better long-term ROI—particularly for teams focused on simplifying workflows.

Still Deciding? Let’s Talk.

Choosing between embedded and non-embedded automation isn’t always straightforward. If you’re not sure which approach fits your environment, a short discovery call with our team can help clarify your needs and priorities. We’re here to help—no pressure, just guidance.

If you’re new to AP automation, be sure to download our guide to selecting the right solution for your organization.

How to Know What’s Right for Your Team

To figure out whether embedded or integrated AP automation is the better fit, consider these questions:

• Are we satisfied with our current ERP’s interface and workflow?
• How important is it to stay within one system for the entire AP process?
• Would a fully ERP-based solution improve usability for our team?
• Do we have IT capacity to maintain and support third-party integrations?
• Do we prioritize centralized control or need more specialized/custom options?
• Should all financial data remain within the ERP environment for compliance or security reasons?

Your answers will help steer your team toward the right type of solution—whether embedded for simplicity, or integrated for flexibility.

Mekorma’s Embedded AP Automation: Designed for Simplicity

At Mekorma, our design philosophy is simple: make AP work better within the tools you already trust. That’s why our Payment Hub is fully embedded in Microsoft Dynamics 365 Business Central and Dynamics GP.

No external portals. No switching screens. No extra logins.

With Mekorma, you can manage the full AP lifecycle—from vendor onboarding and invoice processing to approvals, printing, and digital payments—directly inside your ERP.

Key benefits include:

• Unified interface for all payment activities
• Built-in role-based security and audit trails
• Seamless adoption with minimal training
• Tools like the Action Board and Shared Services for multi-entity environments

Final Thoughts: Embedded = Alignment, Not Limitation

Choosing embedded automation doesn’t mean sacrificing flexibility—it means building on a foundation that works.

By embedding AP tools directly into your ERP, you gain clarity, reduce risk, and give your team a smoother experience from start to finish.

At Mekorma, we design solutions that reduce friction and increase confidence—so your systems work with you, not against you.