Top Ecommerce Inventory Management Tools for 2025

In the fast-paced and ever changing world of eCommerce, effective inventory management is crucial for successful eCommerce operations. This is important whether you are selling on Shopify and need to carry out Shopify inventory management, or if you are multichannel/selling on Amazon. Keeping track of stock levels, processing orders efficiently, and minimizing overstock or stockouts can mean the difference between profit and loss, and the difference between being cash positive and chasing those MCAs. As online shopping continues to evolve, businesses really need reliable tools to streamline their operations and meet customer expectations without unnecessary delays or disruptions.

Choosing the right inventory management software is crucial for eCommerce businesses of all sizes. The right solution can automate key processes, integrate seamlessly with sales channels, and provide real-time insights into stock levels, helping businesses make informed decisions and carry out real time accounting. From demand forecasting to multi-warehouse tracking, modern inventory management systems offer features that can reduce costs and improve efficiency.

Today, the inventory management software landscape is more advanced than ever, with cloud-based accessibility, robust automation capabilities, and AI-driven analytics using eCommerce accounting software to provide more alternatives and capabilities than ever. The sky really is the limit. 

This article explores the best eCommerce inventory management solutions available, helping you find the perfect fit for your business needs.

What is eCommerce Inventory Management Software?

Ecommerce inventory management software is a digital solution designed to help online businesses track, organize, and manage their stock levels- in other words, to carry out eCommerce inventory management. It automates key inventory-related processes such as stock replenishment and SKU management, in order to make sure that brands have the right products available at the right time (nobody wants stockouts or overstocks). These platforms often integrate with eCommerce platforms and marketplaces, providing a centralized dashboard for monitoring inventory in real time. This additionally enables you to carry out real time eCommerce accounting, enabling you to price properly and not to cross finance your SKUs. 

As online businesses scale, manual inventory management becomes unsustainable. And by manual I mean just using a spreadsheet. A well-implemented inventory management system allows businesses to adapt to changing demand, manage supplier relationships effectively, and streamline logistics. By reducing operational bottlenecks and ensuring accuracy, these solutions help ecommerce retailers maximize profitability and maintain a competitive edge in an increasingly crowded market. And folks, when differentiation is low (usually is), and entry barriers practically non-existent, you need to be on the top of your game to win.

Best eCommerce Inventory Management Software Solutions (2025)

Selecting the right inventory management software is essential for optimizing stock control, streamlining operations, and ensuring seamless order fulfillment. Let's explore some of the best eCommerce inventory management software solutions available in 2025, detailing their features, benefits, and potential drawbacks to help you make an informed decision.

Sortly

Sortly is an inventory management system designed to help businesses track stock levels across several locations. It integrates with various platforms.

Pros:

• Easy-to-use interface
• Highly customizable, allowing brands to adjust the setup based on their needs 
• QR code scanning for fast inventory tracking 

Cons:

• Requires a steep learning curve
• The integration with bookkeeping software is cumbersome

Best for: Small to medium-sized businesses looking for a straightforward inventory management tool, and enterprises that need multiple levels of access and capabilities. 

Cost: Sortly's prices range between $24 and $149 per month (with enterprise pricing higher).

Trunk

Trunk is an inventory management solution built for eCommerce businesses. It provides real-time insights enabling businesses to remain informed about their stock levels at all times. This is particularly useful for businesses selling on multiple platforms like Shopify, Amazon, Etsy, and WooCommerce.

Pros:

• Real-time stock syncing 
• Easy to set up and use
• Hands-on customer service

Cons:

• Lack of reporting and inability to export products to audit
• Limited searching and sorting options

Best for: Small commerce businesses selling across multiple platforms

Cost: Trunk's prices range between $35 and $279 per month for their essential plan (pro plan or higher volume is more costly).

Netstock

Netstock is an inventory optimization tool that helps businesses maintain optimal stock levels across various sales channels. Its features include demand planning, inventory optimization, inventory forecasting and more.

Pros:

• Integration with various systems
• Straightforward dashboard for monitoring key inventory metrics

Cons:

• Lacks vendor report cards
• Limited learning modules after the onboarding

Best for: SMBs that need inventory optimization and planning tools.

Cost: Pricing is based on your inventory value.

Lightspeed Retail

Lightspeed Retail is an inventory management solution designed for eCommerce brands. It provides real-time inventory tracking, automated stock updates across channels, and detailed analysis that helps businesses make informed decisions. 

Pros:

• Integrates with several systems and card payment terminals
• 24/7 customer support 

Cons:

• The setup requires a lot of configurations 
• No recurring billing and serial number tracking options

Best for: Retail and eCommerce businesses looking for a combined POS and inventory management system.

Cost: Lightspeed Retail's prices range between $89 and $289 per month (billed annually).

inFlow

inFlow is a cloud-based inventory management solution that automates inventory tracking and replenishment to help brands manage stock more efficiently. It includes several features that ensure brands can account for inventory levels in real-time, including user alerts when stock must be ordered. 

Pros:

• User-friendly interface with easy implementation
• Product-level visibility that helps decisions making

Cons:

• Lacks year end inventory count reset
• The crosstalk between inFlow and accounting software is not ideal

Best for: Small and medium-sized businesses looking for a budget-friendly inventory tracking system.

Cost: inFlow's prices range between $149 and $799 per month (billed annually).

InventoryIQ (by Finaloop)

InventoryIQ is the first real-time inventory management system built right into an eCommerce accounting software. It streamlines inventory management with centralized PO and vendor management, real-time COGS tracking, and unparalleled visibility into inventory by warehouse and SKU.

Pros:

• Real-time COGS tracking by channel, warehouse, and SKU
• Automated landed cost calculations for better profit margin analysis
• Direct syncing with sales channels and financial transactions
• Centralized purchase order (PO) and vendor management

Cons:

• Might not be a fit for very early stage brands with minimal inventory

Best for: eCommerce businesses that prioritize accurate cost tracking and financial visibility

Cost: InventoryIQ's price depends on projected gross revenue for the next 12 months, starting with $100 per month.

Key Features to Look for in the Best eCommerce Inventory Management Software

When evaluating inventory management solutions for your eCommerce business, certain features can distinguish truly transformative platforms from basic tracking tools. The best solutions offer a range of features designed to optimize operations, improve efficiency, and support growth. From real-time inventory tracking to automated forecasting, these tools help businesses reduce errors, streamline processes, and ensure seamless order fulfillment.

If you’ve managed to stay with us until now, kudos! See below the key features that make inventory management software effective.

Real-Time Inventory Tracking

Real-time inventory tracking is essential for maintaining accurate stock levels. This feature ensures that online stores, warehouses, and sales platforms are always in sync, and gives business owners a clear picture of their stock availability at any moment, making it easier to manage supply chain operations.

It also helps prevent costly problems like stockouts and overstocking. Stockouts can lead to lost sales and frustrated customers, while overstocking ties up valuable capital in unsold products. If you have to err to one or the other- it generally is better to stockout vs overstocking, but that’s just a matter of opinion. Capital tied up in inventory is really, really tough. 

In general, by keeping a precise record of inventory levels, businesses can optimize restocking schedules and avoid unnecessary holding costs. And last but not least, real-time tracking also improves customer experience by ensuring that listed products are actually available for purchase, reducing order cancellations and backorders.

Multi-Channel Synchronization

For eCommerce businesses selling across multiple platforms—such as Shopify, WooCommerce, Amazon, and Etsy—inventory synchronization is crucial. Multi-channel synchronization ensures that stock levels update instantly across all sales channels when a purchase is made. This eliminates the risk of overselling products on one platform while inventory runs out on another.

Centralized inventory management also improves operational efficiency by consolidating stock data from various sales channels, warehouses, and fulfillment centers. Businesses can track product movement across different platforms without manually updating inventory records, reducing errors and improving accuracy. Additionally, automated synchronization makes it easier to expand into new marketplaces, as businesses can scale without the fear of mismanaging stock levels.

Automated Reordering & Forecasting

Managing inventory manually can be time-consuming and error-prone, especially when handling large volumes of stock. Automated reordering eliminates the guesswork by generating purchase orders when stock reaches a predefined threshold. This ensures that products are replenished on time, preventing stockouts while avoiding excessive inventory buildup. Some advanced systems also factor in supplier lead times and order history to optimize the reordering process.

AI-driven demand forecasting takes inventory management to the next level by analyzing past sales data, seasonal trends, and market fluctuations to predict future demand. By leveraging predictive analytics, businesses can adjust purchasing decisions proactively rather than reactively. This reduces the risk of overstocking slow-moving items or running out of high-demand products, ultimately improving cash flow and supply chain efficiency.

Reporting & Analytics

Data-driven decision-making is critical for optimizing eCommerce operations, and robust reporting and analytics tools provide the insights needed to stay ahead. Inventory management software generates detailed reports on sales trends, stock turnover rates, and product performance. By analyzing these metrics, businesses can identify best-selling products, detect slow-moving inventory, and make informed decisions about restocking and pricing strategies.

Custom dashboards further enhance visibility by allowing businesses to track key performance indicators (KPIs) tailored to their specific needs. Whether monitoring revenue growth, supplier performance, or order fulfillment rates, these dashboards provide a comprehensive view of inventory health. 

SKU Management & Barcode Scanning

Efficient SKU (Stock-keeping unit) management is crucial for accurate inventory tracking and product identification. By assigning unique SKUs to each item, businesses can quickly locate and manage stock, reducing confusion and errors. SKU management helps streamline warehouse operations, making it easier to track inventory levels, manage product variations, and categorize items based on attributes such as size, color, and brand.

Barcode scanning contributes to inventory accuracy by enabling quick and error-free data entry. Instead of manually inputting product information, brand operators can scan barcodes to update stock levels, check product details, and process orders faster. This reduces the likelihood of human error and speeds up order fulfillment, improving overall efficiency. 

Accounting & Financial Integration

Effective inventory management is not just about tracking stock levels and replenishing products – it also requires accounting and financial management knowledge. 

Managing inventory operationally ensures businesses can place purchase orders, restock efficiently, and control unit costs. However, the financial aspect of inventory management – tracking costs per unit (i.e., the landed costs), calculating profit margins, and maintaining accurate financial records – is just as important for understanding your financial health and making informed business decisions.

A key aspect of financial inventory management is understanding Cost of Goods Sold (COGS) and landed cost per unit. COGS represents the direct costs associated with producing or purchasing the goods a business sells, and it directly impacts profitability. Landed cost per unit includes all costs incurred to bring inventory to a warehouse, such as product costs, shipping in fees, insurance, taxes, tariffs, and handling fees. 

If these costs are not accurately calculated and accounted for, businesses risk setting incorrect pricing models, misjudging profitability, and producing unreliable accounting reports.

Automated bookkeeping for inventory costs provides significant benefits, particularly for eCommerce businesses handling large volumes of transactions. Manually tracking expenses, adjusting COGS, and allocating landed costs can be time-consuming and prone to error. 

Inventory management software that integrates with accounting systems streamlines this process by automatically calculating inventory costs, syncing financial data with accounting platforms, and generating real-time profit and loss reports. This level of automation not only ensures accuracy in financial reporting but also provides business owners with clear insights into cash flow, profit margins, and tax liabilities.

A great example of an integrated solution is InventoryIQ by Finaloop, the first real-time inventory management system built directly into an eCommerce accounting platform. Unlike standalone inventory tools, InventoryIQ ensures that COGS calculations, landed costs, and inventory tracking are always in sync with financial data. This eliminates costly errors and gives eCommerce brands real-time visibility into their inventory by warehouse and SKU. 

With features like centralized purchase order and vendor management, automated real-time COGS tracking, and bill of materials management, businesses can scale efficiently without relying on spreadsheets or manual calculations. By choosing a solution like InventoryIQ, brands gain full financial and inventory control, empowering them with the data they need to optimize operations and profitability.

Common Challenges in eCommerce Inventory Management & How Software Helps

Managing inventory in eCommerce comes with various challenges that can impact customer satisfaction, operational efficiency, and profitability. From stock discrepancies to inaccurate demand forecasting, these issues can lead to lost sales, excessive costs, and frustrated customers. Without the right tools in place, businesses may (and most likely will) struggle to keep up with inventory demands, especially as they scale and sell across multiple channels.

Fortunately, eCommerce inventory management software is designed to address these challenges through automation, real-time tracking, and data-driven insights. By leveraging the right technology, brands can minimize errors, optimize stock levels, and streamline operations. Below, we explore some of the most common inventory management challenges and how software solutions help overcome them.

Overselling & Stockouts

Overselling occurs when a business sells more products than it has in stock, often due to delays in inventory updates across multiple sales channels. This can lead to customer dissatisfaction, order cancellations, and reputational damage. Stockouts, on the other hand, happen when a business sells out of a product faster than it can be replenished, resulting in missed sales opportunities and lost revenue. Managing stock across multiple warehouses and sales platforms manually increases the risk of these issues, especially for brands operating at scale.

Inventory management software prevents overselling and stockouts by offering real-time inventory synchronization across all sales channels. Automated stock updates ensure that product availability is always accurate, reducing the risk of selling out-of-stock items. Additionally, low-stock alerts notify businesses when inventory is running low, allowing for timely restocking before a stockout occurs. Some advanced solutions also offer automated reordering based on historical sales data, ensuring that businesses maintain optimal stock levels without overcommitting resources.

Manual Errors & Inefficiencies

Relying on manual processes for inventory tracking can lead to costly mistakes. Manually entering stock levels, updating spreadsheets, or processing orders increases the likelihood of human errors, such as incorrect stock counts or duplicate entries. These inefficiencies slow down order fulfillment, create inconsistencies in inventory records, and require additional time to identify and correct errors. As eCommerce businesses grow, manual methods become increasingly unsustainable, leading to operational bottlenecks and wasted resources.

Ecommerce inventory management software eliminates manual errors by automating key inventory processes. Barcode scanning, automated stock updates, and real-time order tracking reduce reliance on manual data entry, ensuring greater accuracy. Integrations with eCommerce platforms and fulfillment centers further streamline operations, allowing businesses to focus on growth rather than fixing inventory discrepancies. By reducing the risk of errors and increasing operational efficiency, inventory software helps brands scale without compromising accuracy.

Inventory Shrinkage & Theft

Inventory shrinkage – caused by theft, miscounts, damaged goods, or supplier fraud – can significantly impact profitability. Whether due to internal theft by employees, external theft during transit, or simple mismanagement, lost inventory leads to financial losses and stock discrepancies. Without proper tracking, businesses may not realize inventory is missing until it becomes a significant issue, making it difficult to identify the root cause and implement preventive measures.

Inventory management software combats shrinkage by improving inventory visibility and accountability. Features like real-time stock tracking, barcode scanning, and audit logs provide brands with a clear view of their inventory movements. Many solutions also include user permissions and role-based access controls, reducing the risk of internal theft by limiting who can modify stock records. Additionally, automated inventory reconciliation ensures that discrepancies are flagged early, allowing businesses to investigate and address potential losses before they escalate.

Poor Demand Forecasting

Inaccurate demand forecasting can lead to two major inventory problems: overstocking and understocking. Overstocking ties up capital in excess inventory, leading to increased storage costs and potential losses from unsold products. Understocking, conversely, results in missed sales opportunities and can damage customer trust if popular products are frequently out of stock. Relying on guesswork or outdated sales data to predict demand often leads to misaligned inventory levels, making it harder for businesses to optimize cash flow and supply chain efficiency.

Inventory management software enhances demand forecasting by leveraging data-driven insights. AI-powered analytics analyze historical sales trends, seasonal fluctuations, and market demand to provide accurate restocking recommendations. By using predictive analytics, businesses can make smarter purchasing decisions, reducing excess inventory while ensuring they meet customer demand. Some solutions even integrate with supplier data, allowing businesses to adjust orders based on lead times and production schedules. 

Final Thoughts on Choosing the Best eCommerce Inventory Management Software

Selecting the right inventory management software is a critical decision that can significantly impact your eCommerce business's operational efficiency and profitability. As we've explored throughout this article, modern inventory solutions offer far more than basic stock tracking – they provide comprehensive tools that synchronize multi-channel operations, automate reordering processes, deliver actionable analytics, and integrate with your financial systems.

By addressing common challenges like overselling, manual errors, inventory shrinkage, and poor demand forecasting, the right software solution can transform potential bottlenecks into competitive advantages. When evaluating options, prioritize features that align with your specific business requirements. Consider your sales volume, number of SKUs, warehouse locations, and growth trajectory. 

For eCommerce brands seeking to eliminate the disconnect between inventory operations and financial management, InventoryIQ by Finaloop offers a uniquely integrated approach. As the first real-time inventory management system built directly into an accounting platform, it provides unparalleled visibility into your inventory costs, COGS tracking, and profit margins – all synchronized automatically with your financial data. 

Ultimately, the best inventory management software is one that grows with your business, adapts to your changing needs, and delivers measurable improvements in efficiency and profitability. Take the time to assess your requirements carefully, leverage free trials when available, and choose a solution that positions your eCommerce business for long-term success.