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Taxes for startup businesses: What founders must know

Early tax choices can reduce your burden and keep you compliant. This guide breaks it down.
Tax
November 11, 2025
|
6 min

Do you know which early choices can cut your federal tax bill and still keep you compliant?

We write this as fellow founders who want clarity, not confusion. This Ultimate Guide gives a plain-English roadmap to federal and state obligations, key filings, and high-value elections that matter in year one.

Federal corporate income for C-corps follows a flat regime and Form 1120 is required annually even with no income. Some states add a recurring minimum franchise charge and a separate corporate income tax. Key dates cluster around late January, mid-March, mid-April, and mid-quarter estimates.

We’ll walk through nexus risks, bookkeeping essentials, R&D credit opportunities, QSBS planning (note: some states do not conform), and how startup costs are capitalized and amortized. If you want help operationalizing compliance, meet Lazo.

Why this ultimate guide matters

Quick, practical clarity around filings and deadlines prevents costly surprises. Founders juggle product, hiring, and runway; missing a return deadline or quarterly estimate creates penalties and distraction.

Remote teams and LatAm–US founders face extra complexity: multiple jurisdictions can trigger filings sooner than expected (think payroll/contractor reports in late January; corporate returns or extensions by mid-March; estimates around mid-April, mid-summer, early fall, and early in the following year).

Some states layer a recurring franchise charge, their own corporate return, and nonconformity with QSBS. We focus on actions you can use today so filings stay clean and timely. For key deadlines, check 2025 US Tax Deadlines.

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Key tax obligations: Federal vs. State

EIN, business tax returns, and who files what

Get registrations right at launch. Secure an EIN immediately; it opens bank, payroll, and state accounts.

Choosing the correct federal return:

  • C-Corporations: Corporate return (Form 1120).
  • Partnerships / multi-member LLCs: Informational partnership return (Form 1065).
  • Sole proprietors / Single-Member LLCs:
    • U.S. resident owner: report business income on Form 1040 Schedule C.
    • Foreign (non-U.S.) owner: file an informational Form 1120 (proforma) with Form 5472 to disclose related-party transactions.
  • S-Corps: Corporate return (Form 1120-S) after election. Note: not available for foreign-owned entities or nonresident shareholders.

How states differ

States vary widely: some impose corporate income plus franchise charges; others use gross-receipts models. Multistate revenue is apportioned by sales, payroll, and property.

Pro tips

  • Align calendars (federal vs. state due dates can differ).
  • Document nexus decisions for diligence/audits.

Strategic tax levers for startups

Entity choice basics: LLC, S-Corp, and C-Corp for tax strategy

  • C-Corp suits venture scale: institutional rounds, stock options, potential QSBS; taxes occur at the corporate level.
  • S-Corp passes income through to owners and may reduce employment tax with reasonable compensation; eligibility and one-class-of-stock rules apply.
  • LLC is flexible; income flows to members, plan for self-employment tax and investor preferences that may later favor a C-Corp.

Model after-tax outcomes at key milestones, plan QSBS early, and remember some states assess franchise charges even with little activity.

State tax nexus for remote teams and distributed operations

Presence (not intent) usually determines whether a state can tax you.

What creates a taxable presence

Remote-first pitfalls: One new hire in a state can create withholding, unemployment, and filing obligations; apportionment then allocates income. Build a hiring checklist that includes registrations and payroll setup.

Learn more in → Minimizing State Income Tax for Remote-First U.S. Startups.

Sales and use tax, SaaS, and multistate compliance (quick view)

Pure SaaS is often non-taxable in certain jurisdictions (e.g., California), but taxable in others like New York or Texas. Downloadable software, physical media, or bundled hardware can also create taxable components. Define your product, split pricing on bundles, and automate rules (SKU matrix + rate updates).

R&D tax credit and other benefits for startups

Claiming R&D credits early can reduce payroll burn and extend runway. Eligible companies may use the federal credit to offset employer payroll taxes when income tax is low. 

Substantiate with short project briefs, time records, and invoices. See more → Claim R&D Tax Credits as a Tech Startup.

NOLs and loss planning: carryforwards, limitations, and state differences

  • Federal NOLs typically carry forward indefinitely, but can only offset up to 80% of taxable income.
  • States vary widely, some suspend or limit use in certain years.
  • Ownership changes may limit usage (IRC §382); maintain year-by-year schedules.

QSBS fundamentals: Section 1202 and state nonconformity

QSBS may exclude a substantial portion of federal capital gains if strict tests are met:

  • C-Corp status
  • Original issuance
  • Gross assets ≤ $50M at issuance
  • Active trade/business
  • Holding period ≥ 5 years

Some states do not fully conform, state gains may still be taxable. Preserve minutes, ledgers, grants, and valuations.


Tax compliance calendar: key startup tax deadlines across the year

Keep a simple rolling calendar with federal anchors:

See our → tax deadlines guide.

Start-up costs, capitalization, and deductions: get treatment right from day one

Separate pre-opening costs from operating expenses. Depreciate tangible property; amortize organizational/start-up costs unless immediate deduction is elected where allowed. Document policies, approvals, and schedules so tax and GAAP stay aligned.

Delaware companies operating in other states: Franchise tax, foreign qualification, and dual obligations

Delaware offers governance advantages; however, when a Delaware company operates in another state, it must register as a foreign entity, open state payroll accounts (if applicable), and file local tax returns. Expect dual obligations—Delaware franchise tax plus the franchise or income tax of the operating state. Register early, keep certificates of authority, and track renewal dates to maintain compliance.

Bookkeeping, payroll, and estimated taxes: preventing costly errors

Close books monthly, reconcile key accounts, and maintain a chart of accounts that separates R&D, capitalization, and operating expenses. Set up payroll accounts before the first hire, classify workers correctly, and schedule estimates to avoid underpayment penalties.

Common mistakes founders make on business taxes and how to avoid them

  • Starting payroll before state registration.
  • Missing payroll/contractor statements in January.
  • Assuming SaaS is never taxable.
  • Ignoring economic nexus after fast growth.
  • Weak capitalization and R&D records.
  • Skipping estimated payments after strong quarters.

Simple checklists for payroll, information returns, nexus, and R&D documentation turn compliance into routine.

How Lazo helps founders stay compliant and reduce tax risk

We turn complex compliance into predictable operations:

  • Rolling calendars and reminders.
  • Nexus reviews and registrations.
  • SaaS sales/use configuration.
  • R&D documentation.
  • Organized workpapers for returns/audits.

We align tax strategy with fundraising and equity plans so attributes survive diligence. Meet our team or schedule a free consultation.

Conclusion

A compliance-first approach makes taxes repeatable and defensible. Keep a living calendar, tight documentation, and monthly closes; preserve NOLs, capture R&D credits early, treat remote hires as state events, and plan QSBS with counsel. We’re ready to help operationalize this roadmap so you can scale with confidence.

Book a call with our Team!

FAQ

What is the difference between federal and state obligations for a new company?

Federal: get an EIN, file the right return (corporate/partnership/individual with business schedule), and pay federal income/payroll taxes.
State: varies by nexus, may include income/franchise/gross-receipts tax, sales & use tax, and employer withholding with state-specific thresholds and deadlines.

How do we choose the right return form for our entity?

Match the entity: C-Corp → corporate return; Partnership/multi-member LLC → partnership return; Sole prop → individual with business schedule; S-Corp → corporate return after election. Weigh investor needs, payroll, and exit plans.

When does it make sense to form a C-Corp for venture growth?

When raising VC, issuing options, and scaling fast. Pros: equity tools, potential QSBS. Cons: corporate-level taxation. Choose if benefits outweigh costs.

What are the main tax considerations for LLCs and S-Corps?

LLC: flexible pass-through; owners may owe self-employment tax.
S-Corp: can reduce self-employment via reasonable compensation; has shareholder/class restrictions.

How is nexus established for remote teams and distributed operations?

Physical presence (employees, office, inventory) or economic presence (sales thresholds/transactions). Remote hires and marketplaces can trigger registrations and filings.

When is SaaS subject to sales tax?

It’s state-specific. Pure SaaS can be non-taxable in some states, but downloads, media, or bundled hardware may be taxable. Classify each SKU correctly.

How do use tax and bundled services affect revenue recognition?

If sales tax wasn’t collected, use tax may apply. For bundles, allocate price between taxable and non-taxable components and document contracts/invoices.

What qualifies for the R&D tax credit and how do we substantiate claims?

Tech-driven work with uncertainty and experimentation. Eligible costs often include wages, supplies, and contract research. Substantiate with project briefs, time tracking, and cost allocations.

Can early-stage companies offset payroll taxes with credits?

Yes, when eligible. Coordinate with payroll to apply credits correctly.

How do net operating losses (NOLs) work after recent changes?

They generally carry forward with annual usage limits; state rules vary. Track NOLs by year and jurisdiction.

What is QSBS and how can founders qualify under Section 1202?

Potential federal gain exclusion if you meet statutory requirements and a multi-year holding period. Some states don’t conform, plan state tax separately.