16 Common Challenges of Business Process Automation

‍In a recent survey by McKinsey, 66% of businesses said automating business processes is one of their top priorities. Why? Because automation can cut operational costs by up to 30% and speed up tasks that used to take hours into just minutes.

Business Process Automation (BPA) is the use of technology to complete repetitive tasks with little to no human input. Think of it as a smarter way to handle things like approvals, data entry, or email responses—without needing someone to do them every time.

As companies grow, so does the need to move faster and work smarter. BPA helps teams save time, reduce errors, and focus on high-value work.

Still, rolling out BPA isn’t always easy. Businesses often face challenges like choosing the right tools, getting employees onboard, or dealing with outdated systems that aren’t ready for automation.

In this article, we will explore 16 common challenges of business process automation and how to overcome them.

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Fundamental Challenges in Business Process Automation

Many businesses face core challenges that, if ignored, can turn automation into a source of frustration rather than progress.

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1. Complexity of Existing Business Processes

Automation works best when applied to streamlined, well-defined processes. When you try to automate inefficient workflows, you're essentially putting a high-speed engine on a broken-down vehicle: you'll just reach problems faster.

Consider a manufacturing company that automated their complex supply chain without first addressing fundamental inefficiencies. Their process involved multiple approval layers and inconsistent documentation. 

Once automated, what was a slow manual mess became a rapid-fire digital disaster. Orders got stuck in automated loops, inventory data became unreliable, and the system generated thousands of error notifications.

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Before implementing automation, map out and simplify your existing processes. Eliminate unnecessary steps, reduce bottlenecks, and standardize procedures. This preparation creates the solid foundation needed for successful automation.

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2. Lack of Process Standardization Before Automation

Automating tasks without standard rules often leads to mismatches, errors, and incomplete results. Let’s say one team logs sales data in spreadsheets, another in a CRM, and a third by email. If you automate follow-ups based on these inputs, the system won’t know which version is correct.

Standardization ensures that every team follows the same procedure, so automation has a solid base to work from. That’s why process mapping tools like Whimsical or Miro are helpful, they allow you to visualize workflows, spot inconsistencies, and create a single source of truth. Once you’ve mapped and cleaned your process, automation becomes far more reliable and scalable.

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3. Integration with Legacy Systems

Older systems often become major roadblocks in your automation journey. Many legacy applications lack APIs or offer limited connectivity options. Their rigid architecture wasn't designed with automation in mind, creating significant technical hurdles.

When faced with these challenges, Robotic Process Automation (RPA) tools like UiPath can serve as effective bridges. These tools mimic human actions to transfer data between systems without requiring traditional integration points, allowing you to automate processes without expensive redevelopment.

If your legacy system does offer an API, you can potentially connect it to no-code platforms like Bubble, Glide, or FlutterFlow. This approach creates a modern interface while leveraging your existing infrastructure.

For systems without APIs, middleware solutions like Zapier and Make can establish connections between your legacy software and modern tools, enabling communication with newer applications and participation in automated workflows.

While these approaches enable automation with legacy systems, they often represent intermediate solutions until you can modernize critical systems.

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4. Managing Large Volumes of Data

Automation systems generate massive amounts of data that can quickly overwhelm traditional storage solutions. As your automated processes run continuously, they produce detailed logs, performance metrics, and transaction records that need proper management to remain valuable rather than becoming digital clutter.

When your data volume expands, both storage and retrieval become challenging. Reports that once took seconds might take minutes or hours, and finding specific information becomes increasingly difficult without proper data architecture.

To address these challenges, robust data pipelines and cloud-based storage solutions like AWS S3 or Google BigQuery should be implemented. These platforms offer scalable infrastructure designed to handle large datasets efficiently while providing powerful analytical capabilities.

No-code platforms like Glide can integrate with these cloud solutions through their API connectors. This allows you to build user-friendly interfaces for interacting with your data while leveraging the power of enterprise-grade data storage. 

For example, you can create a Glide app that visualizes key metrics from your BigQuery database or allows users to search through archived automation records stored in AWS.

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5. Ensuring Data Quality

Automation is only as effective as the data it processes. When your systems run on incomplete, incorrect, or outdated information, even the most sophisticated automation workflows will produce flawed results. Poor data quality becomes amplified through automation, leading to costly errors and diminished trust.

Consider a common scenario: Your marketing automation sends personalized emails based on CRM data. If that data contains duplicates, incorrect emails, or outdated preferences, your automation might send multiple conflicting messages to the same person, contact people who've opted out, or address customers by the wrong name. What should improve customer experience instead damages your reputation.

Before implementing automation, establish data validation protocols:

• Perform comprehensive data cleansing to correct existing records
• Implement validation rules that prevent incorrect data entry
• Create automated quality checks that flag potential issues
• Establish regular data audits to maintain quality

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Organizational and Strategic Challenges

Beyond technical barriers, many automation efforts fail due to internal misalignment or poor planning. Here are key organizational challenges you should be ready to face.

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6. Misalignment Between Technical and Business Stakeholders

When IT teams and business leaders aren't aligned, automation projects can quickly derail. Business teams may push for fast results without understanding technical limitations, while developers may build systems that don’t match real-world needs. This disconnect often results in wasted time, budget overruns, and underused tools.

Collaboration is key.

Successful Business Process Automation (BPA) begins with both sides understanding each other’s goals.

Business leaders should clearly explain the “why” behind automation and what problem they are solving, while IT teams translate that into a practical solution. Workshops, shared documentation, and co-ownership of the process help bridge the gap.

Tools like Notion, Miro, or even shared Slack channels can keep communication flowing. When both teams are aligned, automation becomes a tool for growth, not a source of frustration.

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7. Resistance to Change Within the Organization

Automation can trigger fear among employees who worry their roles may become obsolete. This fear often leads to resistance, slow adoption, or even sabotage of new systems. It’s not the technology that fails, it’s the lack of trust and communication.

To overcome this, leaders must focus on managing change. Start by clearly explaining how automation will help, not hurt, your team. For example, automating data entry allows employees to focus on problem-solving or customer service. Involve key staff early in the process so they feel a sense of ownership over the change.

Training also plays a significant role. Ensure everyone knows how to use the new tools and understand how they benefit their daily work. A phased rollout with opportunities for feedback allows time to adjust and build confidence. When people feel secure, they support automation instead of fearing it.

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8. Hiring the Wrong Partners to Build Automation Systems

Selecting the wrong partner for your automation project can lead to wasted resources, failed implementations, and missed opportunities. Many businesses make the mistake of choosing vendors based solely on cost or impressive sales pitches, only to discover midway that their partner lacks the necessary expertise or experience.

Watch for these red flags when evaluating potential automation partners:

• They promise unrealistically quick implementation timelines without thorough process analysis
• They propose generic solutions without taking time to understand your specific business context
• They lack relevant case studies or references in your industry
• Their team seems to have technical skills but limited business process knowledge
• They cannot clearly explain their methodology or approach in terms you understand

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Hire LowCode Agency to Build Custom Automation Solutions

At LowCode Agency, we've built over 330 custom solutions across diverse industries using leading no-code platforms like Bubble, Glide, FlutterFlow, and Make. Our approach begins with understanding your unique business processes before recommending appropriate solutions.

The right partner should demonstrate both technical capability and business acumen. They should ask detailed questions about your current processes, involve your team in requirements gathering, and provide a clear implementation roadmap with defined milestones. 

Most importantly, they should position themselves as your partner in transformation, not just a vendor selling a service.

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Technical and Financial Challenges

Even with the right strategy and tools, automation can hit technical and budget roadblocks. Let’s look at the most common ones.

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9. High Initial Implementation Costs

Getting started with BPA often involves upfront costs such as software licenses, employee training, cloud infrastructure, and sometimes consulting fees. These expenses can feel overwhelming, especially for small and mid-sized companies.

To reduce risk, many businesses begin with small pilot projects. This allows teams to test tools, measure impact, and refine workflows before a full rollout.

Now, no-code platforms like Bubble, Glide, FlutterFlow, and Make also support building scalable automation solutions. They let you design workflows, connect databases, and automate tasks without writing code. Since these platforms are faster to build on, they reduce both time and cost compared to traditional development.

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10. IT Security Concerns

Automation platforms often manage sensitive information like customer records, financial data, and internal processes. This makes them prime targets for threats like data breaches, unauthorized access, or weak API protections.

To stay secure, businesses should follow best practices like using Zero Trust architecture, strong encryption, and role-based access controls. Firewalls, activity logs, and regular audits also help reduce risks.

Many no-code platforms build these protections in. For example,

• Bubble uses SSL encryption, audit trails, and privacy rules.
• Glide offers granular data access
• FlutterFlow integrates secure Firebase authentication.

While no system is foolproof, choosing platforms with built-in security features helps safeguard your automation efforts.

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11. Handling Exceptions and Special Cases

Automated systems work well with routine tasks but often have trouble with unusual cases. If your automation cannot manage an exception, like a missing invoice or a complicated client request, it may stop the process or make an incorrect decision.

For example, consider a finance team that automates payment approvals. If a vendor submits a duplicate invoice, the system might approve it again unless someone points out the problem.

This is why human oversight is still important. You need to create workflows that notify team members when something is not normal. Adding manual review steps or smart notifications can help manage exceptions without slowing down the entire system.

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12. Maintaining Process Flexibility

Over-automation can be a problem when workflows become too rigid. If your system can’t adapt to new regulations, customer needs, or market trends, it can slow you down instead of speeding things up.

For example, if a company automates its onboarding process, a small change in compliance rules might require weeks of reconfiguring the automation, leading to delays.

That’s why flexibility is important. Choose tools that allow you to adjust processes without having to rebuild everything from scratch. No-code platforms are great for this. They enable non-tech teams to quickly change logic, update rules, or modify data flows, keeping your business agile as things change.

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Long-Term Challenges in Business Process Automation

Once automation is set up and running, the real work begins. You need to make sure it grows with your business and keeps providing value over time.

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13. Training Employees to Work Alongside Automated Processes

Automation doesn’t replace teams; it changes how they work. Employees need to understand how automated systems operate, when to intervene, and how to fix issues when they arise. This requires developing new skills in data handling, decision-making, and process management.

Upskilling is essential. Provide regular training sessions, create internal documentation, and use practical tools to help teams feel confident and capable. 

When employees understand the “why” and “how” of automation, they are more likely to embrace it and help it succeed. Continuous learning ensures that your team evolves alongside your automation tools, rather than falling behind.

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14. Scalability Issues with Automation Tools

Many automation solutions that perform brilliantly during initial deployment struggle to keep pace as your business grows. What works perfectly for 50 transactions daily might fail completely when processing 5,000, creating bottlenecks exactly when you need efficiency most.

These scalability issues typically emerge when processing volumes increase, workflows become more complex, or you need to extend automation to additional departments. Suddenly, systems that ran smoothly begin experiencing slower response times, synchronization problems, or even complete failures.

The solution lies in modular automation design, breaking processes into smaller, independent components that can be scaled individually. This approach allows you to strengthen specific parts of your workflow without rebuilding the entire system.

We implemented this strategy when building BuildGenius for Scott Crawford, a growing real estate development company. Their document management system needed to handle increasing project volumes as the business expanded. 

By creating a modular architecture within Glide, we developed a solution that reduced document retrieval time by 45% while increasing their capacity to manage simultaneous projects by 70% within six months.

When designing your automation strategy, prioritize solutions that offer clear scaling paths. This foresight will prevent the need to replace systems entirely as your business grows.

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15. Continuous Monitoring and Adaptation of Automated Processes

Automation isn’t a “set it and forget it” solution. Over time, processes change, customer needs shift, and tools evolve. If you don’t monitor and update your systems regularly, your automation can become outdated or start causing errors.

Set up a schedule to review workflows monthly or quarterly. Track failures, delays, and usage logs to catch issues early. Use tools like Make or Zapier dashboards to monitor the health of your processes, and gather team feedback to identify any pain points.

Adapting is just as important as setting up your automation. A well-maintained automation system remains efficient, accurate, and aligned with your business goals, saving you from costly reworks later.

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16. Difficulty in Measuring ROI for Business Process Automation

One of the toughest long-term challenges is proving that automation is actually paying off. Many businesses struggle to measure how much time, money, or effort BPA saves. Without the right metrics, it’s hard to justify further investment.

To track ROI, focus on metrics like task completion time, error rates, employee hours saved, and customer response times. You can also measure cost reductions from fewer manual tasks or improved data accuracy.

We’ve recently built a free tool that helps calculate automation ROI using metrics like time saved, error reduction, and cost impact. 

With this tool, you can enter the manual tasks that are taking up your team's time and estimate how many hours you could save by automating them.

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Conclusion

Business Process Automation (BPA) offers many benefits, but it also comes with challenges. Issues like complex workflows, outdated systems, data quality problems, and team resistance can slow down even the best automation efforts. Without careful planning, clear communication, and the right tools, businesses risk wasting time and resources.

Successful BPA is not just about technology; it's about strategy. It requires teamwork, ongoing training, and a commitment to monitoring and improvement. Businesses that view automation as a continuous process rather than a one-time setup are more likely to succeed.

Ready to overcome these automation challenges? Let's build solutions that drive real results for your business. Book a free consultation call with us today so we can start planning your future business decisions.