Amazon FBA: The main challenges (and how to overcome them)

From hidden fees to limited visibility, many fast-growing brands face the same challenges when relying solely on Fulfilment by Amazon. 

Rising costs caused 65% of businesses to hike their own prices, and is one of many blockers to growth that countless brands run into. 

The good news is, with many of these challenges, they’re just growing pains. With the right strategy (and technology), you can stay on Amazon and stay in control. 

Let’s look at the key Amazon FBA challenges for growing businesses. 

1. Losing control of brand experience 

When Amazon fulfils your orders, it also controls packaging, delivery, and communication. That means your carefully built brand experience ends up hidden in an Amazon Prime box. 

Because of this, you can lose recognition and direct relationships, key ingredients for long-term loyalty and repeat purchases. 

 
The antidote 

• Run a hybrid fulfilment strategy. Keep FBA for marketplace reach but fulfil DTC and wholesale orders elsewhere to personalise packaging and messaging. 

• Integrate your channels through a unified order management system, ensuring consistent experiences for customers. 

2. Rising costs and unpredictable fees  

Amazon announced FBA fee increases for February and June 2025, with standard-sized items seeing average fee rises of 4-6%, and oversized items facing rises of up to 8%. 

Also introduced were surcharges for ‘inbound placement’ and ‘low inventory,’ meaning costs could scale faster than sales if not monitored by businesses. 

For bulky or seasonal SKUs, these charges can add up quickly and wipe out profits. 
 

The antidote 

• Track your total landed costs – including storage, prep, and removal fees – in real time using integrated analytics. 

• Move slower or oversized stock into third-party fulfilment with lower fees. 

• Simplify your SKU range during peak periods, focusing on faster-moving, higher-margin products. 

3. Limited visibility and data access

FBA dashboards are great for orders, but not the best for insights. You can see what sells, but not the reasons why. Amazon doesn’t share much about fulfilment performance or customer behaviour, either. 

This means that forecasting can often become guesswork, and brands struggle to spot trends or react to delays quickly enough. 

 
The antidote 

• Integrate Amazon sales into a multi-channel order management system for added visibility. 

• Sync inventory, performance, and customer data across platforms like Shopify, WooCommerce, and your fulfilment partner. 

• With a unified dashboard, you can forecast demand, balance stock, and make faster, data-driven decisions.

4. Returns and refunds – the silent margin killers

Amazon’s returns system is designed well for consumers, but often doesn’t serve value to FBA brands. You rarely control communication, and you might not see stock again if it’s marked as ‘unsellable.’ 

Each return can therefore chip away at your profits, and inconsistent experiences can frustrate the customers who expect instant refunds.

The antidote 

• Manage returns through an external fulfilment provider or integrated fulfilment platform to process returns faster and resell recovered stock. 

• Connect customer service tools to your fulfilment data to keep shoppers informed. 

• Keep FBA for simple, high-volume SKUs, but handle premium or complex items yourself to protect brand experience.

5. Storage limits and seasonal pressures

During Q4, Amazon can restrict inventory capacity to prevent warehouse overflow. Sellers are rated on IPI (Inventory Performance Index) scores, which can impact your ability to send more stock. 

Future planning and careful inventory management are essential ahead of peak periods, as stockouts, lost sales, and ‘out of inventory’ listings can seriously harm your business when demand peaks. 

 
The antidote 

• Use external fulfilment centres to store overflow inventory and replenish FBA in bursts. 

• Automate restocking using sales data and lead times to avoid overpaying for storage. 

• Forecast demand using tools that predict demand based on historical sales data and seasonal influences. 

• Create a split strategy: FBA for fast sellers, independent fulfilment for slower or seasonal lines. 

6. Channel dependence and growth limits 

Relying solely on Amazon means you’re bound to its rules, algorithms, and fees. One policy change or unexpected account suspension can send sales grinding to a halt, damaging your business. 

Amazon is incredibly efficient, but it’s wise to have a back-up plan if things were to go wrong. 

 
The antidote 

• Use a multi-channel fulfilment model that integrates Amazon into your wider network, rather than the other way around. 

• Choose a fulfilment partner that can sync Amazon with your eCommerce store, wholesale channels, and returns systems for a unified operation. 

FBA isn’t the problem – but total reliance can be 

Amazon FBA works brilliantly for what it’s meant to do: fulfil Amazon orders fast. But as your business scales, reliance on only Amazon can become a bottleneck. 

Owning your data, spreading your fulfilment, and connecting every channel through technology means you can enjoy the benefits of Amazon without surrendering total control. 

When you’re scaling fast on Amazon, you need more than just shipping – you need strategy. 

Our Amazon fulfilment solution allows you to integrate your store, manage inventory and orders in one hub, and scale globally without losing brand identity. 

Whether you’re FBA, FBM, or a hybrid, we make sure your operations stay efficient and your brand stays heard.