7 Best Ecommerce Inventory Management Software in 2025

If you sell online, you know the struggle. Running out of stock means losing sales, but overstocking kills your cash flow. And if you're selling across multiple channels like Shopify, Amazon, and Etsy, keeping inventory accurate feels like a full-time job.

With global ecommerce sales expected to hit $7 trillion in 2025, the competition is fiercer than ever. The right inventory management software ensures you never oversell, prevents costly mistakes, and helps you scale without headaches. In this guide, we’ll cover the seven best inventory management tools to keep your stock in sync and your business growing.

What features should your ecommerce inventory management software have?

You can't choose the best inventory management software for e-commerce without considering its features. 

You’ll need software that syncs with 3PL partners, dropshipping suppliers, and multiple sales channels to know what’s in stock and where it’s stored.

The right features will help optimize your supply chain by giving insights into when to restock and how much you need. Here’s what to focus on:

1. Real-time inventory sync

Your software should keep stock updated across all channels, preventing overselling and stockouts. If you sell a handmade bag on Etsy, the system should automatically update inventory on Shopify. Without this, you risk selling out-of-stock items and disappointing customers.

2. Multichannel order management

Your software should be able to consolidate orders from different platforms into one dashboard for easier tracking. Without it, tracking orders across multiple channels will lead you to use different connector apps for each platform, leading to disintegrated data.

3. Integration with accounting software

Platforms like Webgility automatically sync inventory costs and sales with QuickBooks. This keeps financial records and inventory accurate without manual intervention. Without integration, you’d spend hours reconciling stock levels with revenue reports.

4. Automated reordering

Your platform should help you automate purchase orders when inventory hits a set threshold, avoiding stockouts. If a best-selling candle drops below five units, the system can auto-place an order with suppliers. Without automation, you might forget to restock and lose sales.

5. Demand forecasting

Your platform predicts inventory needs based on past sales trends, preventing overstock and shortages. If holiday sales spike every December, the system can suggest ordering more in advance. Without forecasting, you may either overbuy or run out at peak times.

6. Returns management

You need to be able to track returned items and update stock accordingly. If a customer returns a dress, the system can mark it as available for resale. Without this, returns create confusion and potential inventory losses.

7. Supplier management

Automates purchase orders, tracks deliveries and provides supplier insights. If a key supplier has delays, the system flags it so you can find alternatives. Without this, missed restocks can disrupt your supply chain.

Top ecommerce inventory management software: A quick overview

Before we dive deep into each tool, here’s a quick review of the best inventory management software for your ecommerce business:

Top 7 ecommerce inventory management software

Once you know which features you need, you can start exploring the best ecommerce inventory management software options for your business.

 Webgility (Best for ecommerce inventory sync and management)

When you’re looking to manage your ecommerce inventory effectively, you need a solution that ensures accuracy and scalability. Webgility is the best ecommerce inventory sync solution for QuickBooks that improves inventory management across multiple sales channels. It seamlessly integrates your sales platforms like Shopify, Amazon, Walmart, eBay, and more with QuickBooks, saving you time and minimizing errors.

You can track stock levels in real-time, automate order processes, manage product listings, and get insightful reports about your business performance. Webgility automates inventory updates, syncs stock levels across multiple channels, and creates purchase orders based on current stock levels, so you never run out of products or oversell.

The software's powerful reporting and performance tracking features give you actionable insights into your sales trends and product profitability, making it an excellent tool for growing your ecommerce business.

Why should you use Webgility for inventory management?

What sets Webgility apart from other inventory management systems is its deep integration with QuickBooks and its ability to manage multiple sales channels in one unified system. Its automated features, like order management and inventory syncing, make it ideal for businesses looking to save time and reduce manual errors. 

You can also track individual products with unique SKUs across different platforms, solving the issue of managing multiple SKUs for the same product in different stores. For products without barcodes, Webgility allows you to manually track and update your inventory without requiring barcode scanning.

Best features

• Multichannel sales sync integration with QuickBooks: Webgility seamlessly integrates your sales platforms with QuickBooks, allowing for accurate financial data and simplified inventory management across all channels.
• Inventory tracking: Real-time inventory tracking helps prevent stockouts and overselling, ensuring you never run into stock discrepancies while keeping customer satisfaction high.
• Multichannel integration: Webgility supports integration with 40+ ecommerce platforms like Shopify, Amazon, and eBay, making it easy to manage inventory across all your sales channels from a single location.
• SKU-level tracking: With SKU-level tracking, Webgility makes it simple to handle multiple SKUs for the same product across different platforms and avoid confusion.
• Barcode scanning: Use a barcode scanner to quickly verify shipments and returns, saving time and ensuring accurate stock counts, so you’re always in the loop on your inventory status.
• Automate product listings: Webgility automates the creation of product listings across multiple channels and integrates them with QuickBooks, saving time and maintaining consistency.

Pros

• Automated reporting helps you understand sales trends and product profitability
• Highly customizable, allowing you to tailor features to your business
• Responsive customer support that addresses concerns quickly and effectively
• Faster than QuickBooks Desktop Connector for Shopify integration

Cons

• Loading times can be slow at times, but it does not significantly impact functionality
• Initial setup might take time to adjust according to the business’s needs

Pricing

• Basic: $59/month per sales channel 
• Pro: $119/month per 2 sales channel

For Webgility’s most recent pricing, check our pricing page.

Here’s what a G2 user said about using Webgility:

2. Unicommerce (Best for SaaS ecommerce enablement)

Unicommerce is a popular ecommerce enablement SaaS platform that supports end-to-end management of operations for brands, marketplaces, and logistics providers. It offers comprehensive solutions for both pre-purchase and post-purchase stages, improving operational efficiency and driving growth.

As one of the best ecommerce inventory management software, Unicommerce helps businesses track inventory across multiple warehouses, analyze detailed inventory reports, receive instant alerts for low-stock items, and much more. In addition, the platform helps with vendor management, ERP integration, and returns/replacement processes, ensuring your operations run smoothly from start to finish.

Best features

• Centralized view: Manage your inventory management with a unified log-in panel, simplifying stock movement and control across multiple sales channels.
• Barcoding: Assign unique identifiers to each unit using system-generated barcodes or QR codes, enabling efficient tracking and location management within the warehouse.
• 270+ plug-and-play integrations: Connect with 270+ marketplaces, carts, logistics providers, ERP, and POS systems to simplify your ecommerce operations.
• Data-driven analytics: Leverage detailed performance reports to analyze your inventory and sales data, making smarter decisions to optimize operations and boost profitability.
• Order routing: Efficiently route orders to specific sales channels while updating and replenishing stock daily for seamless order management.
• SKU/item level bundling: Create product bundles to introduce combo packs, expanding your reach and showcasing products to a wider customer base.

Pros

• Organize inventory smartly by moving seasonal or slow-moving products based on demand with inventory slotting
• Stay informed with custom alerts that track stock-related information and provide timely updates for your workflow

Cons

• Some users say they had to reconcile payments manually as the software does not handle payment tracking yet

Pricing

• Standard, Professional & Enterprise: Custom pricing

Refer to Unicommerce’s pricing page for updated pricing.

3. Cin7 (Best for multichannel inventory management)

Built for manufacturers and product sellers, Cin7 is an excellent choice for small businesses, whether you're a retailer, wholesaler, or online seller. The platform’s Connected Inventory Performance (CIP) connects your entire product lifecycle, from sourcing and production to sales and fulfillment, providing real-time visibility and automating workflows. 

With over 700 integrations, including popular platforms like Shopify, Amazon, and QuickBooks, Cin7 allows you to manage your inventory across multiple channels effortlessly. 

Cin7’s ForesightAI also helps with demand forecasting, automating reorder processes and minimizing waste. Its advanced reporting tools give you valuable insights into sales trends and inventory costs, allowing you to make data-driven decisions for more efficient business operations.

Best features

• Connected inventory intelligence: Cin7 ForesightAI allows you to predict demand, prevent stockouts and overstock, and fine-tune your orders for timely stock availability, keeping you ahead of competitors.
• Multiple integrations: With 700+ integrations, including Xero, QuickBooks, Shopify, Amazon, and ShipStation, Cin7 ensures smooth communication and unified operations across all your platforms.
• Automated invoicing: Cin7 integrates with QuickBooks and Xero to automate invoicing and payment tracking, helping you stay organized and allowing you to focus on business growth.

Pros

• Streamline warehouse operations with automated stock movement
• Automated invoicing with QuickBooks and Xero
• Barcode scanning (in the pipeline) for a streamlined pick-and-pack process

Cons

• Complex and time-consuming setup process requiring significant support
• Occasional glitches in syncing orders or inventory between systems

Pricing

• Standard: $349/month per 5 users
• Pro: $499/month per 10 users
• Professional: $999/month per 15 users

Check Cin7’s pricing page for updated pricing information.

4. Netstock (Best for supply and demand planning)

As a best-of-breed supply and demand planning software, Netstock claims to deploy AI to optimize forecasting, reduce stock-outs, and lower inventory levels by more than 25%. With its intuitive dashboard, you can instantly view key performance indicators like stock vs. model stock, fill rates, and excess stock.

Best features

• Inventory monitoring: Netstock lets you monitor key inventory metrics in real-time with a single dashboard, including stock vs. model stock, fill rates, stock-outs, and excess stock. You can also take advantage of AI-driven insights from the Opportunity Engine to identify and address inventory issues instantly and customize reports to enhance daily decision-making.
• Inventory classification: Automatically classify SKUs based on sales and velocity, allowing you to focus on high-demand, high-profit products and reduce overstocking of low-performing items.
• Replenishment planning: Generate optimized orders and replenish stock faster by predicting demand and supply fluctuations using Netstock. Easily transfer surplus stock between locations for balanced inventory across all sites.

Pros

• Get unlimited custom reports to refine your daily operations
• Review and issue orders efficiently to prevent stock-outs and excess stocks
• Easy integration with your ERP system to quickly ingest data

Cons

• Some users say it would be helpful to add additional columns like SKU code and BRAND to views such as stocked out, potential stock out, and stock holding

Pricing

• Custom pricing

Refer to Netstock’s pricing page for updated pricing.

5. Fishbowl Inventory (Best for inventory, warehousing, and manufacturing)

Fishbowl Inventory provides a real-time, automated inventory management platform that allows you to track inventory by various factors such as quantity, weight, serial number, or expiration date. You can easily scan barcodes, monitor stock levels across locations, and keep track of your assets' availability. 

The platform also allows you to manage costing, pricing models, and landed costs in one place. It integrates seamlessly with QuickBooks Online, streamlining the process from quoting a customer to generating sales orders, packing, and shipping. 

With its ability to provide detailed reports, Fishbowl helps you make informed decisions while reducing manual entry and errors. 

Best features

• Stock monitoring: Monitor stock levels in real-time to reduce excess inventory and replace dead stock with high-demand items, keeping your inventory lean and efficient.
• Sales synchronization: Update stock levels instantly with each sale across all sales channels, ensuring accurate order fulfillment and preventing stockouts.
• Account reconciliation: Sync Fishbowl with QuickBooks for up-to-date financial data, helping you make informed purchasing decisions, forecast future needs effectively, and maintain hassle-free bookkeeping.

Pros

• Integrates seamlessly with QuickBooks to quote, process orders, and generate shipping labels
• Intuitive workflow keeps inventory accurate and up-to-date

Cons

• The setup process can be time-consuming and sometimes confusing
• Adding new tracking fields to the system can be cumbersome
• The lack of attachment storage at the inventory level is a limitation

Pricing

• Basic Inventory, Advanced Warehousing & Advanced Manufacturing: Custom pricing

Check out Fishbowl Inventory’s pricing page for more information on pricing.

6. Zoho Inventory (Best for MSMEs and large-scale corporations)

For businesses looking to manage orders, track inventory, and handle GST billing in India, Zoho Inventory offers a comprehensive solution. It helps businesses of all sizes, from MSMEs to large corporations, keep tabs on stock levels, manage sales and purchase activities, and monitor payments. The software allows you to manage multiple warehouses, track item movements, and transfer items across locations. 

Zoho Inventory also integrates with barcode scanners, making it easier to manage SKUs, serial and batch numbers. You can even monitor the expiry dates for your products. Additionally, the software provides various reports that give you insights into inventory aging, vendor payments, sales details, and inventory valuation, which can be easily downloaded or shared.

Best features

• Centralized warehouse management: Zoho Inventory lets you control stock across multiple warehouses, optimizing product availability for faster shipping and delivery in ecommerce businesses.
• Multichannel integration: Zoho Inventory integrates with major ecommerce platforms like Shopify and Etsy, as well as payment gateways like PayPal and Razorpay to manage inventory, orders, and payments from a single platform, improving efficiency in running an online store.
• Batch tracking: With Zoho Inventory's serial and batch tracking, ecommerce businesses can keep precise records of spare parts, saleable items, and expiry dates. This helps reduce errors, manage stock rotation, and guarantee that products are always in stock and fresh, enhancing customer trust and reducing returns.
• VAT compliance management: Generate VAT-compliant sales and purchase transactions and ensure compliance with VAT standards by adding customers, vendors, and items.

Pros

• Wide range of integrations with platforms like Shopify, PayPal, and Zoho CRM
• Automated order management helps reduce manual errors 
• Accurate batch and serial number tracking for better compliance and product traceability

Cons

• Limited in-depth reporting with room for improvement in report details
• Slow support process that adds more manual work 

Pricing

• Standard: $39/month per 2 users
• Professional: $99/month per 2 users
• Premium: $159/month per 2 users
• Enterprise: $299/month per 7 users

Refer to Zoho Inventory’s pricing page for updated pricing.

7. Shopify (Best for building and managing ecommerce stores)

If you're running a store on Shopify, you'll have access to built-in inventory management features included in your monthly plan. You can set up inventory tracking, view your stock levels, and adjust them directly in Shopify’s Inventory area. Shopify also allows you to check the history of any inventory adjustments made to products and variants. 

In the Inventory Reports section, you can analyze changes in stock levels to track trends. If you'd like to stay on top of low stock, Shopify offers inventory alert apps in their App Store to notify you when stock is running low.

Best features

• Inventory tracking: View on-hand, available, committed, unavailable, and incoming stock in one place for better control.
• Multi-location inventory management: Distribute inventory efficiently across up to 1,000 warehouses, fulfillment centers, and stores.
• Inventory automation: Use Shopify Flow to hide out-of-stock products, receive low-stock alerts, and streamline updates.

Pros

• Integrates with everything you need to run your store
• User-friendly and simple to set up and manage
• Large community with plenty of resources and support

Cons

• Limited access to data for small businesses, forcing you to upgrade for full access

Pricing

• Basic: $29/month per 10 inventory locations
• Shopify: $79/month per 10 inventory locations + 5 additional staff accounts
• Advanced: $299/month per 10 inventory locations + 15 additional staff accounts
• Plus: Starts at $2,000 per 200 inventory locations + unlimited staff accounts

For their most recent pricing, check Shopify’s pricing page.

Simplify ecommerce inventory management with the right software

Inventory management is crucial for the success of any ecommerce business. Selecting the right software can simplify your processes, saving time and money as your business grows.

The most important part of choosing the right software is that it offers the needed features and can scale as your business expands. Webgility is one such tool that syncs and automates inventory across platforms, giving real-time stock updates and preventing overselling. It also integrates with ecommerce stores, marketplaces, accounting software, and shipping providers, reducing manual work and keeping stock levels accurate. 

So, what are you waiting for? Sign up today to get started!

Frequently Asked Questions

How do I choose the right inventory management software for my business size?

To choose an inventory management system, consider your order volume, number of sales channels, and automation needs. Smaller businesses may benefit from simple, cost-effective tools, while larger operations require advanced forecasting and supplier management.

What hidden costs should I watch out for when selecting a tool?

The most savvy business owners are aware of hidden platform costs: charges for additional users, integrations, or API access, as well as extra fees for high-order volumes. While subscription fees may seem straightforward, these additional costs can add up quickly and impact your bottom line.

Which inventory management software is best for multichannel sellers?

You should choose tools with seamless integrations for Shopify, Amazon, Etsy, and third-party logistics. Options like Webgility and Cin7 excel at real-time inventory syncing across multiple platforms.