There’s no single ‘best’ accounting software for labs—and anyone promising a top ten list is missing the point. The real question is which type of system fits your stage of growth. Pick well and you gain clean fund tracking, reliable asset registers, and reports that stand up to audits.
Free & Open-Source Tools
Some labs turn to open-source accounting to cut costs and retain more control over how the software is used. GnuCash (Windows, macOS, Linux | Desktop) offers a no-cost way to set up formal double-entry accounting. It is stable and widely used in small organizations, with enough features for basic ledgers and reports. The tradeoffs are a configuration process that can be complex, support limited to community forums, no cloud access, and little automation.
Odoo (Windows, macOS, Linux | Cloud) is modular enterprise resource planning (ERP) software. These systems connect functions such as accounting, payroll, procurement, and inventory in one platform. Odoo delivers this through small applications that can be added as needed. The flexibility appeals to IT-savvy teams, but audit trails, compliance controls, and grant reporting are not part of the core package. Odoo is available as Community (open source, free, self-hosted) and Enterprise (commercial, with more modules, support, and cloud hosting).
Entry-Level Cloud Systems
Small labs often turn to entry-level cloud accounting for ease of use and integration with banks or payroll. QuickBooks (Windows, macOS | Cloud) is the most common choice. It supports basic invoicing and project tags, and is easy for non-specialists to adopt. The limits show up quickly: splitting payroll across grants is awkward, asset tracking is minimal, and reporting can require manual workarounds.
Xero (Windows, macOS | Cloud) emphasizes a clean interface and includes a built-in fixed asset register. It offers simple project costing through a paid add-on. The drawback is that only two tracking categories are allowed, which makes it hard to manage multiple grants or funding sources.
Nonprofit & Grant Accounting Systems
Once multiple grants enter the picture, labs need systems that treat each funding stream as distinct. Blackbaud Financial Edge NXT (Browser | Cloud) creates a separate ledger for every grant, with budgets and reports that align with funder requirements. It is reliable for grant accounting but less suited to internal R&D or broader lab finance.
Sage Intacct (Browser | Cloud) takes a similar approach but relies on dimensions—tags applied to transactions—to sort expenses by grant, project, or department. This avoids long account codes but adds complexity. Setup usually requires outside expertise, and costs rise with scale.
ERP Systems for Growing Labs
Growing R&D firms face more complex needs: fixed assets, payroll allocations, and project-level costing. Unlike open-source platforms, which rely on customization and in-house support, commercial ERPs from vendors such as Microsoft, Oracle, and others package these features together with vendor support and built-in controls. They cost more to implement but offer audit logs, role-based access, and depreciation schedules out of the box.
Conclusions
Accurate accounting gives labs the basis for better decisions. For more on how labs turn financial planning into a tool for growth, such as through budget design and optimizing revenue cycles, continue reading Lab Manager.
