Best Inventory Management Software That Integrates With QuickBooks (2025 Guide)

If you’re a small product-based business using QuickBooks, you’ve probably run into a common issue: inventory tracking just isn’t built for makers. QuickBooks is great for accounting—but when it comes to managing raw materials, tracking batches, or calculating accurate cost of goods sold (COGS), things can get messy fast.

That’s where inventory management software comes in. The right tool integrates smoothly with QuickBooks while giving you the inventory features you actually need to stay organized, price confidently, and grow your business.

Here’s a quick roundup of the best inventory management software options that integrate with QuickBooks, with a spotlight on our top pick—Craftybase—designed specifically for small-scale manufacturers and handmade sellers.

1. Craftybase – Best for Handmade Sellers and Small Manufacturers

✅ Best for: Crafters, makers, and small DTC brands that manufacture their own products
🔗 QuickBooks integration: Yes (syncs invoices & expenses)
💡 Standout feature: COGS tracking built specifically for product-based businesses

If you’re a maker who manufactures your own products—whether it’s skincare, jewelry, candles, or anything in between, Craftybase is built for you. Unlike generic inventory tools, Craftybase automatically calculates your COGS using actual material and labor costs from your batch production history. That means you always know your true costs and profit margins—without spreadsheets or guesswork.

With Craftybase, you can:

• Track raw materials and finished goods in real time
• Automatically calculate your rolling COGS
• Manage batch production and material usage
• Keep sales, expenses, and inventory synced with QuickBooks
• Prepare for tax time with ready-made reports

Why it’s great with QuickBooks:
Craftybase connects directly with QuickBooks Online to sync your purchase data (COGS and more coming soon!). That means no double entry, no data silos—just clean, up-to-date financials and accurate inventory tracking side-by-side.

🏆 Best for product makers who need real inventory control—not just a spreadsheet add-on.

👉 Try Craftybase Free for 14 Days

2. inFlow Inventory – Best for Wholesale-Focused Businesses

✅ Best for: Wholesalers, retailers, and B2B sellers
🔗 QuickBooks integration: Yes (via connector)
💡 Standout feature: Barcode scanning & B2B showroom features

inFlow Inventory offers powerful inventory and order management tools, especially for businesses selling wholesale. It handles multi-location stock, purchasing, and invoicing—and offers a B2B portal for large clients. The QuickBooks integration connects sales and financial data but may require a middleware tool depending on your plan.

3. Katana – Best for Small Manufacturers Scaling Up

✅ Best for: Manufacturers who need production planning tools
🔗 QuickBooks integration: Yes
💡 Standout feature: Visual production scheduling

Katana is a solid choice for small manufacturers who are growing and need visual production planning and inventory control. It integrates with QuickBooks Online and popular ecommerce platforms. While it’s more robust than some entry-level tools, it can feel overpowered for smaller makers or those without complex workflows.

4. Zoho Inventory – Best for Budget-Conscious Businesses

✅ Best for: Small businesses with simple inventory needs
🔗 QuickBooks integration: Yes
💡 Standout feature: Multi-channel sales tracking at a low price

Zoho Inventory is an affordable option with integrations across sales channels like Amazon, eBay, and Shopify. It’s best for businesses that primarily resell products rather than manufacture them. While it connects to QuickBooks, it doesn’t handle raw material tracking or detailed COGS calculations out of the box.

Final Thoughts: Which Inventory Software Is Best for You?

If you’re looking for an inventory management system that plays nicely with QuickBooks and gives you visibility into your real product costs, Craftybase is your best bet—especially if you make what you sell.

It’s the only tool on this list designed specifically for handmade sellers and small manufacturers. From raw material tracking to batch production to pricing guidance, Craftybase helps you take control of your numbers so you can run a more profitable, less stressful business.

👉 Start your free trial of Craftybase today and see why thousands of product makers trust us to manage their inventory and costs.