Best B2B Invoicing Software for 2025

Managing invoices at scale in a B2B environment isn’t just about sending PDFs and tracking due dates anymore. In 2025, invoicing software must handle automation, compliance, integration with CRMs and ERPs, and, in some cases, support global e-invoicing mandates.

Whether you’re billing for enterprise services, B2B SaaS subscriptions, digital agencies, or specialized labs, your invoicing tools should automate the process, reduce errors, and give your finance team real-time visibility into payment pipelines.

In this guide, we’ll break down the best B2B invoicing software by use case, show how these tools stack up on features, and help you pick the right one for scaling operations.

🔎 What Is B2B Invoicing Software?

B2B invoicing software helps businesses send and manage invoices at scale—automating the process of billing other companies. It goes far beyond simple receipt generation, offering tools for bulk billing, complex payment terms, purchase orders, and approval workflows tailored to business clients.

Unlike B2C systems, these platforms are built to handle the intricacies of large-scale operations and long-term contracts. They often integrate with accounting tools like QuickBooks, Xero, or NetSuite, streamlining the entire financial cycle from quote to cash.

Today’s top B2B invoicing tools typically offer:

• 📄 Custom invoice templates and flexible contract terms
• 🔗 API access for syncing with ERPs and PM platforms
• 🌍 Multi-currency support and tax compliance (e.g. EU e-invoicing)
• 💳 Multiple payment options: ACH, wire, cards, more
• ⏱️ Automated invoicing and payment reminders
• 🔍 Full audit trails for procurement and finance teams

🔧 Best B2B Invoicing Software (2025 Picks)

🚀 Spotlight: Everhour for Project-Based B2B Invoicing

If you’re a SaaS team, consultancy, or creative agency billing by the hour or by deliverables, Everhour‘s time tracker is one of the best invoicing solutions available.

Why?

• It integrates directly into ClickUp, Asana, Trello, Basecamp, and Jira
• You can log time directly on tasks, tag billable hours, and pull that data into client-ready invoices
• Supports hourly, flat-fee, or retainer-based billing models
• Syncs with QuickBooks, Xero, or FreshBooks for accounting (and with other QuickBooks alternatives)

🧪 Best B2B Lab Invoicing Software

Labs—especially in biotech, diagnostics, or research—need more than a PDF invoice. You often need to:

• Bill per test or assay, often with variable pricing
• Handle reimbursements or funding-based invoicing
• Generate HIPAA-compliant financial records

Top picks for B2B lab invoicing:

• SimplePractice (for mental health and medical labs)

• Jane App (chiropractic, PT, diagnostic labs)
• LabWare LIMS + ERP integration
• Custom billing modules via Salesforce Health Cloud

🤔 What Makes a Great B2B Invoicing Tool in 2025?

B2B invoicing isn’t just about sending a bill — it’s about scaling finances with precision. Here’s what your tool absolutely needs:

• ⚙️ Automation: Recurring billing, late payment nudges, and smart scheduling save hours of admin work every week.
• ✅ Custom approval workflows: Multi-layer approvals are common in B2B. Your tool should let finance ops define internal review flows before an invoice is sent.
• 🌍 Compliance & localization: From e-invoicing in India to EU VAT rules — your invoicing software must handle global requirements out of the box.
• 🕵️ Audit trails & history logs: Crucial for regulated or enterprise companies. Every edit or send action should be logged and visible.
• 🔗 CRM & accounting integrations: Your invoicing system should plug into your stack — think QuickBooks, Xero, HubSpot, ClickUp, Salesforce.

🌐 What About Global E-Invoicing for B2B?

Governments in 2025 are increasingly moving to mandatory e-invoicing, where your software must:

• Generate machine-readable formats (like XML or UBL)
• Connect to government platforms for validation
• Timestamp and archive invoices for multi-year audit windows

Recommended tools for e-invoicing compliance:

• Invoiced (supports India, Mexico, EU Peppol)
• Comarch (enterprise e-invoicing, SAP integration)

• Tipalti (e-invoicing + payments + tax ID verification)

🔚 Final Thoughts

If your company sends dozens (or hundreds) of B2B invoices per month, manual billing isn’t scalable. From time-based billing to automated collections and compliance with global regulations, invoicing software is a backbone for finance ops in 2025. Choose a tool that integrates into your core systems, supports approval flows, and doesn’t require hours of configuration.

If you run a service business, agency, or SaaS team, Everhour is the ideal choice, especially if you already manage tasks in ClickUp or Asana. It’s more than just invoicing. It’s billing, reporting, time tracking, and client ops in one system. Ready to upgrade your B2B time tracking and invoicing stack?

👉 Try Everhour for free!

❗ Learn how to write an invoice with our guide!

❗ Learn more about the best B2B email marketing platforms and the best time tracking tool for marketing agencies out there!

Make sure to learn how to do B2B market research!