Clerky vs Stripe Atlas vs Bonsai: Best Legal Formation Tools for Software Dev Shops

The Quick Answer

Choose Clerky if you're forming a Delaware C-Corp and plan to raise venture capital — it's the gold standard for VC-ready documentation including SAFE notes, 83(b) election support, and IP assignment agreements pre-configured for startup equity. Choose Stripe Atlas if you're an international founder who needs a U.S. business entity, bank account, and Stripe payment processing set up in under 48 hours. Choose Bonsai if you're a bootstrapped dev shop or freelance agency that needs ongoing client contract management — MSAs, SOWs, NDAs, invoicing, and time tracking — in one platform.

Clerky: The VC-Startup Formation Standard

Clerky ($599 for full package) is specifically designed for startups that expect to raise venture capital. The package includes Delaware C-Corp formation, a standard equity plan with 10 million authorized shares, IP assignment agreements for founders and future employees, a Proprietary Information and Inventions Agreement (PIIA), offer letter templates, and SAFE note templates.

For a bootstrapped software development agency, Clerky is likely overkill. Its C-Corp structure means you'll pay corporate income tax at 21% on retained earnings (vs. pass-through taxation for an LLC/S-Corp), and dividends are taxed again at the shareholder level — the 'double taxation' issue. Unless your dev shop will raise VC funding, build a software product, or bring on co-founders with equity stakes, the C-Corp structure Clerky creates costs more in taxes than it saves.

Where Clerky shines for dev shops: if you're building productized software on the side of client work, or if you have co-founders who need a formal equity split, Clerky's documentation package is worth every dollar. The PIIA and IP assignment workflows are particularly clean.

Stripe Atlas: Speed and Global Access

Stripe Atlas ($500 one-time) opens a Delaware C-Corp or LLC, a Mercury business bank account, and a Stripe payment processing account simultaneously — all remotely, without needing a U.S. Social Security Number. This makes it the top choice for international founders (developers in India, Brazil, Eastern Europe, or elsewhere) who want to bill U.S. clients in USD.

Atlas includes standard startup legal documents, a U.S. mailing address, and EIN registration. Stripe's banking partner Mercury (mercury.com) is genuinely excellent for tech companies — free, no minimums, with clean integrations to QuickBooks, Pilot, and Rippling.

For U.S.-based dev shop founders, Atlas offers less differentiation. You can open a Mercury account directly for free, register your LLC with your state for $100–$300, and get an EIN for free from IRS.gov — achieving the same outcome for less. Atlas's primary value is removing friction for non-U.S. founders who would otherwise need to navigate complex international incorporation workflows.

Bonsai: Purpose-Built for Software Agencies

Bonsai ($24/month for Freelancer, $39/month for Professional) is the only platform in this comparison designed specifically for ongoing agency operations rather than one-time formation. It includes: attorney-reviewed MSA and SOW templates with IP assignment clauses, NDA templates, proposal generation with e-signature, time tracking, invoicing with automatic payment reminders, and a client portal.

For a software dev shop, Bonsai solves three daily operational problems. First, it provides a professional contract-to-payment workflow: send proposal → client signs online → project starts → track time → invoice automatically → get paid. Second, its templates are specifically reviewed for software agency use cases including IP ownership clauses, change order processes, and limitation of liability provisions. Third, it's affordable enough to use from day one — you don't need to land a $100K project to justify the subscription.

Bonsai's Freelancer plan ($24/month) handles up to unlimited clients and projects. The Professional plan ($39/month) adds subcontractor management — useful when you're bringing in specialized contractors for specific project needs.

Head-to-Head Comparison

Cost: Clerky ($599 one-time), Stripe Atlas ($500 one-time), Bonsai ($24–$39/month).

Entity type: Clerky (Delaware C-Corp only), Stripe Atlas (Delaware C-Corp or LLC), Bonsai (works with any entity, not a formation tool).

Best for: Clerky (VC-backed startups, co-founder equity), Stripe Atlas (international founders, speed), Bonsai (bootstrapped agencies, ongoing contracts).

IP protection: Clerky (excellent — PIIA + IP assignment for founders/employees), Stripe Atlas (standard documents only), Bonsai (excellent for client MSAs — attorney-reviewed clauses).

Ongoing value: Clerky (one-time), Stripe Atlas (one-time), Bonsai (continuous — contracts, invoicing, time tracking).

Tax structure: Clerky (C-Corp double taxation risk for agencies), Stripe Atlas (can form LLC, avoiding this), Bonsai (formation-agnostic).

Recommended Setup for Different Dev Shop Scenarios

Bootstrapped solo dev shop (U.S.-based): Register your LLC with your state online ($100–$300), open a Mercury bank account directly (free), get your EIN from IRS.gov (free), and subscribe to Bonsai ($24/month) for all client contract management. Total first-year cost: under $600, not counting state annual fees.

Bootstrapped dev shop with 2+ co-founders: Same as above but spend $500–$1,000 with a startup attorney to draft a custom Operating Agreement with equity vesting schedules, buyout provisions, and a founder IP assignment clause. This is one document where the $500 attorney fee is significantly cheaper than the $50,000+ dispute it prevents.

Dev shop planning to raise VC: Use Clerky ($599) for the full C-Corp formation package. The VC-ready documentation is worth it — you'll eventually pay these costs anyway through your attorney during funding diligence, and Clerky does it faster and cheaper upfront.

International founder building a dev shop to serve U.S. clients: Use Stripe Atlas ($500) for fast U.S. entity formation with a Mercury bank account, then add Bonsai ($24/month) for contract management.

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