Best 1099 Software for Small Businesses in 2025

I recommend Zoho Books for 1099 reporting because it’s easy to mark vendors as 1099-eligible, and its interface is user-friendly with helpful automation. If your business is using other Zoho tools, such as Zoho CRM and Zoho Payroll, integration adds efficiency. Its role-based access controls also make managing sensitive data secure and straightforward.

The downside is that Zoho Books doesn’t directly support e-filing, corrections, or less common 1099 variants like 1099-LTC or 1099-CAP. It also lacks built-in tools for managing e-delivery consent. For full 1099 filing capabilities, including IRS/state e-file and amendments, I recommend integrating Zoho Books with Tax1099, which fills these gaps.

Standout features and use cases

• E-commerce businesses: Tracks payments to third-party sellers, dropshippers, and freelancers, ensuring accurate 1099 reporting and reducing the risk of IRS penalties or missed filing obligations.
• Freelance agencies: Monitors payments to contractors and automates 1099-NEC reporting, reducing manual work and ensuring timely tax filing.
• Real estate firms: Tracks commission payments to agents throughout the year, making it easy to generate accurate 1099 forms at year-end.
• Marketing consultants: Categorizes vendor expenses for services like design, copywriting, or SEO, ensuring clean 1099-MISC documentation and better expense tracking.

Bookkeeper360 offers personalized bookkeeping services with a dedicated accountant, and this hands-on support made it easy for me to stay compliant without diving into the details myself. The clear pricing for business tax filings adds to the convenience. If you’re seeking expert-led service, Bookkeeper360 is a strong choice for outsourced 1099 filings with bookkeeping assistance.

However, it falls short in transparency on its 1099 compliance features. It’s unclear whether it supports corrections, e-delivery consent tracking, or varying 1099 form types. Since a dedicated accountant handles filings, you won’t get visibility into those tools. For more control and clarity, Avalara is the better choice. It supports all 1099 variants and compliance tasks with detailed, user-friendly features.

Standout features and use cases

• Construction companies: Tracks project-based payments throughout the year, simplifying 1099-NEC filings; its dedicated accountants ensure proper classification of labor costs, making it more accurate than self-service platforms.
• Healthcare practices: Ensures that vendors — such as private clinics and medical offices that often pay freelance specialists and outsourced firms — are properly flagged for 1099s while managing complex expense categories.
• Nonprofits: Has a team that helps navigate nonprofit-specific account rules.

I recommend Tax1099 if your business needs 1099s and no additional services. It offers flexible, affordable filing with strong compliance tools like TIN matching, e-delivery consent tracking, and corrections handling. It supports a wide range of 1099 variants and integrates smoothly with platforms like QuickBooks and Xero.

Where it falls short is in its dated user interface and initial learning curve. It also lacks white-label branding, which is a drawback for accountants managing client-facing portals. Avalara is a strong alternative for a smoother user interface.

Standout features and use cases

• Professional services firms (e.g., architects, engineers): Offers real-time TIN matching and corrections tools, which are more robust and responsive than the features in basic filing software; those are great for firms working with subcontractors for design, drafting, or technical consulting.

• Event management companies: Features bulk-import and API features that beat manual-entry tools by offering scale and speed for busy teams prepping hundreds of forms used for independent vendors like photographers, caterers, AV technicians, and other specialty experts.

• Hospitality groups (hotels, restaurants, venues): Provides multi-user, role-based access, optimal for multi-location businesses paying entertainers, maintenance crews, and seasonal workers.

Avalara’s Track1099 platform offers a reliable, feature-rich solution for 1099 filing. It supports real-time TIN matching, state filings, e-delivery with consent tracking, and a wide range of form types — including 1099-LTC and 1099-CAP.

However, it lacks white-label branding, which limits its appeal for firms wanting a branded client experience. Its interface can also feel dated and less intuitive for new users. In these areas, Tax1099 excels, offering branding customization and a more user-friendly design.

Standout features and use cases

• Businesses with frequent vendor changes: Offers comprehensive W-9 management tools, enabling you to collect, store, and manage vendor information securely; can also automatically transfer vendor details from W-9 forms to 1099 filings, minimizing manual data entry and ensuring accuracy.

• Organizations requiring year-over-year data retention: Retains and transfers data from previous years, facilitating easy updates and reducing the need to re-enter information annually; this feature is particularly beneficial for organizations with recurring vendors or contractors.

• Enterprises with high volume filing needs: Can handle large volumes of 1099 filings efficiently; ability to import data via CSV, API, or integrations with common accounting systems like QuickBooks and Xero, which streamlines the filing process for enterprises dealing with numerous contractors or vendors.

• Businesses requiring secure and compliant e-delivery: Ensures IRS-compliant e-delivery by obtaining recipient consent before electronic delivery and automatically resending corrected forms when necessary; this enhances security and compliance, reducing the risk of penalties.

QuickBooks Online simplifies 1099 prep by tracking vendor payments and flagging eligible contractors automatically. Its built-in reports and integration with e-filing partners like Tax1099 make filing easy. The platform is cloud-based, is collaborative, and includes consent tracking and corrections, which makes it a convenient all-in-one solution for small to midsize businesses, particularly those already using QuickBooks.

However, it lacks support for lesser-used 1099 forms like 1099-LTC or 1099-CAP and requires third-party tools for e-filing. I recommend looking into Tax1099 and Avalara for broader form support, built-in TIN matching, and better customization for professional use.

Standout features and use cases

• Freelancers managing subcontractors: Offers an easy, affordable setup without needing separate tools; also, it integrates contractor payments with bookkeeping, unlike more complex 1099-specific platforms.

• Companies with recurring vendor payments: Automatically tracks and categorizes recurring payments to freelancers or vendors.

• In-house accounting teams preparing for filing season: Supports internal teams that prepare data ahead of filing with built-in reports (1099 Summary/Detail) and role-based access; in comparison, competing platforms often lack collaboration tools or require exporting/importing spreadsheets.