10 best B2B invoicing software in 2026 (compared)

Quick summary

If invoicing is eating your team's time, you're likely dealing with manual price lists or invoices that don't reflect your brand. The best B2B invoicing software automates this while keeping invoices accurate. Top picks include SparkLayer for B2B eCommerce invoicing, Sufio for multi-currency invoices, and Bill.com for full AP and AR automation.

For more, explore our best practice guides.

Choosing the right B2B invoicing software

Multiple price lists, varied payment terms, cross-currency issues, VAT differences. Wholesale invoicing is complex by nature, and all of it needs to work smoothly.

Getting there starts with the right software. One that generates accurate invoices automatically, reflects your brand, and fits your existing systems, instead of creating extra manual work.

This SparkLayer guide covers 10 of the best B2B invoicing tools available right now, including which platforms they work best with and what each one charges.

Why trust us

SparkLayer powers B2B operations for 3,500+ brands across food and beverage, apparel, and industrial sectors. We built invoicing directly into our B2B eCommerce platform, so we know firsthand what wholesale brands actually need from an invoicing tool, not just what looks good on a features page.

Read our story to learn more about why we built SparkLayer this way.

10 best B2B invoicing software to automate wholesale billing in 2026

1. SparkLayer

SparkLayer is built for B2B eCommerce brands who want invoicing as part of a connected wholesale experience, not a bolt-on tool. Invoices generate automatically alongside orders, customer groups, and price lists, so your finance and sales processes run from the same system. It's the strongest fit for brands already running (or planning to run) wholesale on Shopify, BigCommerce, or Wix.

Key features

• Automated invoice generation: invoices are created automatically the moment a B2B order is placed, with no manual entry required from your finance team.
• Native accounting sync:SparkLayer Unify connects invoices directly to your accounts software, keeping orders, payments, and balances reconciled in real time.
• Customer group pricing: invoices reflect the exact pricing and terms assigned to each customer group, with no separate price sheet to maintain.
• Branded invoice templates: invoices match your store's look and feel, and customers can view or download them anytime from their account area.

Pricing

**Free: **$0/month **Growth: **$149/month (includes invoicing) 14-day free trial on all paid plans

2. Sufio

Sufio focuses purely on professional invoicing for Shopify merchants. It integrates with SparkLayer directly, making it a natural pairing for brands that want polished, compliant invoices without leaving their existing B2B setup.

Key features

• Customisable templates: invoices are professionally designed and fully customisable, so they carry your branding without requiring any design work from your team.
• Multi-currency and multi-language: invoices automatically display in the customer's local currency and language, built in for brands selling across multiple regions.
• Automated generation from Shopify orders: invoices are created the moment a Shopify order is placed, removing the need for manual creation entirely.
• Compliance-first design: invoices meet accounting and tax requirements out of the box, which is why Sufio is popular with accountants and finance teams.

Pricing

• From $7/month

3. Square

Square brings its well-known ease of use to invoicing, with a free plan that includes unlimited invoices. It suits small and mid-sized businesses that want a working invoicing tool without a steep learning curve.

Key features

• Unlimited free invoicing: the free plan includes unlimited invoices with no monthly cap, making it a genuinely usable option rather than a stripped-down trial.
• Pre-built industry templates: ready-made templates for retail, hospitality, and beauty businesses get you sending professional invoices within minutes of signing up.
• Real-time invoice tracking: track invoice status as it happens, with automated reminders sent to customers whose payments are overdue.
• POS and hardware integration: invoicing connects directly with Square's point-of-sale and hardware, useful for sellers running both in-person and online sales.

Pricing

• From $0/month

4. Intuit QuickBooks

QuickBooks is best known as accounting software, but its invoicing functionality holds up well on its own. For brands wanting one platform to cover invoicing and broader financial management, QuickBooks is hard to beat.

Key features

• Recurring invoices: set up invoices to generate and send automatically on a schedule, with payment tracking handled alongside them with no manual chasing.
• VAT submissions to HMRC: higher plans submit VAT returns directly to HMRC, removing a separate compliance task for UK-based brands.
• Full accounting suite: invoicing sits inside a complete accounting platform, so brands get bookkeeping, payroll, and reporting in one subscription.
• Financial insight tools: built-in reporting gives visibility into cash flow and outstanding invoices, useful for brands managing finances beyond invoicing alone.

Pricing

• From $38/month

5. Order Printer Pro

Order Printer Pro is a Shopify-native app focused on getting professional invoices and documents into customers' hands automatically. It's a strong, low-cost option for Shopify merchants who don't need a full invoicing platform.

Key features

• Customisable templates: invoice templates can be styled to match your brand, with full customisation available for merchants comfortable with some back-end coding.
• Automatic PDF delivery: invoice PDF links are sent to customers automatically after checkout, reducing reliance on your sales or support team.
• Multi-currency and VAT support: invoices display the correct currency, VAT, and translated content automatically, built for merchants selling internationally from Shopify.
• Bulk printing: print invoices in bulk directly from the Shopify admin, POS, or a mobile device, useful for high-volume order days.

Pricing

• From $0/month (paid plans from $10/month for 500 orders)

6. Xero

Xero is a trusted name in small business invoicing, with strong mobile functionality and one-click payments for customers. It's a solid choice for brands that need flexibility and speed.

Key features

• Mobile-first invoicing: create and send invoices directly from your phone, with customers able to pay in a single click from wherever they are.
• Bulk invoice drafting: draft and edit multiple invoices at once, saving time for brands sending a high volume of invoices regularly.
• Credit notes and reconciliation: issue credit notes and reconcile account balances easily, keeping your books accurate without extra manual checking.
• Progress monitoring: track the status of multiple invoices at a glance, so nothing slips through the cracks as volume grows.

Pricing

• From $29/month, with a discount at $5.80 for the first 3 months

7. FreshBooks

FreshBooks is built for service businesses and brands that want invoicing to feel client-friendly and professional. It's particularly strong for brands that bill the same clients repeatedly.

Key features

• Professional templates with online payment: invoices come with clean, client-friendly design and built-in online payment links, speeding up how fast you get paid.
• Automated reminders and recurring invoices: payment reminders and recurring invoices run automatically, removing the need to chase the same clients manually each cycle.
• Double-entry accounting: Plus plans and above include double-entry bookkeeping alongside invoicing, useful for brands wanting more financial accuracy.
• Client portal: clients can log in to track their own invoice and payment history, reducing the volume of status-check emails your team receives.

Pricing

• From $23/month

8. Zoho Invoice

Zoho Invoice stands out for being free to use, with no cap on invoices for businesses under a revenue threshold. It includes multi-currency support, making it a strong budget pick for brands selling internationally.

Key features

• Unlimited free invoicing: the free plan supports unlimited invoices for businesses under a revenue threshold, with no feature-stripped trial period attached.
• Multi-currency and multi-language: invoices display in the customer's currency and language automatically, included even on the free plan with no upgrade required.
• Recurring invoices and client portal: set up recurring billing with automated reminders, while clients self-serve through a portal to view their own history.
• Zoho ecosystem integration: connects directly with Zoho CRM, Books, and Analytics, useful for brands already running other Zoho products.

Pricing

• From $0/month

9. Bill.com

Bill.com (now branded BILL) is an invoicing software that also includes accounts payable and receivable automation capabilities. Its automation features make it ideal for B2B brands managing both incoming bills and outgoing invoices.

Key features

• Two-way accounting sync: data flows automatically between Bill.com and QuickBooks, Xero, or NetSuite, removing the manual reconciliation most invoicing tools require.
• Automated AP and AR workflows: approval chains for both bills owed and invoices issued run automatically, configurable to match how your finance team already works.
• Multiple payment methods: customers and suppliers can pay or be paid via ACH, wire transfer, or virtual card, all managed from one platform.
• Custom user roles: assign specific permissions across payables and receivables, useful for finance teams where different people manage different sides of the process.

Pricing

• From $45/user/month

10. Invoice Ninja

Invoice Ninja is the open-source option on this list, appealing to brands that want full control over their invoicing data and setup. The self-hosted version is free, with paid cloud plans for brands that don't want to manage their own server.

Key features

• Free self-hosted version: run Invoice Ninja on your own server with no software licence fee, giving you full control over your invoicing data.
• Multi-currency and multi-language: invoices automatically adapt to the customer's currency and language, included even on the free self-hosted tier.
• Client portal with document upload: clients can upload supporting documents and view proposals directly through a self-service portal, reducing back-and-forth email.
• Time tracking and project management: link time tracking and project data directly to invoices, useful for brands billing based on hours or milestones.

Pricing

• Free (self-hosted)
• Ninja Pro: $14/month (or $140/year)

How do I choose the right B2B invoicing software for my eCommerce business?

Now you've seen the options, here's what to weigh up before deciding on B2B invoicing software for your business. Key features to prioritise include:

• Customisable invoices that reflect your brand's identity
• Automated and manual options to suit your workflow
• Branded templates for a polished, professional look
• Downloadable versions for customer records
• All-in-one platforms that integrate with your existing systems

Ready to find the right B2B invoicing software?

Whether you’re a growing brand just getting started with wholesale or an established hybrid merchant looking to streamline processes, the right invoicing tool can add infinite value! From complete eCommerce solutions like SparkLayer to accounting-led tools like QuickBooks, there’s a huge range of great B2B invoicing apps designed to fit your business…

Interested in how we can support your wholesale set-up - including B2B invoicing? Book a demo with our team now!

Pricing is correct at the time of this post going live. Pricing may change, so it's always best to check each provider's website directly.

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Lucy Vinestock

Marketing Manager, SparkLayer

Lucy’s background in Marketing covers the entire eCommerce spectrum, and she joined SparkLayer in December 2023 to supercharge our efforts. From content and partner marketing to data analysis and SEO, Lucy is overseeing our full Marketing strategy. When she’s not colour-coding spreadsheets, she’s probably up a mountain, at a yoga class, or cooking up a storm in the kitchen.