Year-End LLC Tax & Compliance Checklist (2026)

Your year-end checklist has six moving parts: clean books, contractor 1099s, the final estimated payment, entity-specific returns, deduction moves that must happen before year end, and compliance filings like the annual report, registered agent renewal, and BOI. Work through them in that order and nothing slips.

Start with the books, because every downstream number depends on them. Reconcile every bank and credit card account against your statements, categorize all expenses, and confirm that owner draws, loans, and reimbursements are recorded correctly. If income and expenses are not reconciled, your deductions, your estimated tax math, and your return are all wrong from the start.

Reconcile every bank and credit card account against its statements, categorize all transactions, and confirm the ending balances match to the dollar before you file anything. Clean books are the foundation of the entire year-end process, because every deduction, estimate, and return draws from them.

Work account by account. Match each cleared transaction to a ledger entry, chase down uncategorized items, and record owner draws, loans, and reimbursements in their own accounts so they do not distort profit. Move out any personal charges that slipped onto the business card. Once the books tie out, your Schedule C or partnership return, your deduction totals, and your final estimated payment all rest on numbers you can defend.

Hand your books to a CPA once they are reconciled and the year has closed, ideally in January so the return is ready before the March 15 or April 15 deadline. Clean books handed over early give the preparer time to catch missed deductions and file without a rushed extension.

Bring the full package: reconciled financial statements, the general ledger, prior-year returns, W-9s and 1099 records, payroll reports if you ran an S-corp payroll, and any asset purchases for depreciation. A foreign-owned LLC flags its Form 5472 obligation up front. The earlier a CPA sees complete records, the more planning stays possible, since some moves such as certain retirement contributions remain open until the extended deadline while others closed on December 31.

Form 1099-NEC is due January 31, both to the contractor and to the IRS. If your LLC paid any unincorporated contractor, freelancer, or service provider $600 or more during the year, you must issue one. Rent and attorney payments follow their own rules on the 1099-MISC.

Collect a signed Form W-9 from every contractor before you pay them, not in January when they have gone quiet. The W-9 gives you the legal name, address, and taxpayer ID you need to file. Payments made through a card or a third-party network like PayPal are reported by the processor on a 1099-K, so exclude those from your 1099-NEC totals to avoid double counting.

The fourth-quarter estimated payment for the prior tax year is due January 15. A single-member LLC is taxed as a sole proprietor by default, so its profit flows to the owner's personal return and the owner pays quarterly estimates directly. Missing the January 15 payment or underpaying across the year triggers an IRS underpayment penalty.

Use the safe-harbor rule to size the payment. Paying 90% of the current year's tax or 100% of last year's tax, rising to 110% if your prior-year adjusted gross income was over $150,000, protects you from the penalty. Our full guide to quarterly estimated taxes walks through the calculation.

If your LLC elected S-corp taxation, confirm the owner took a reasonable salary through payroll during the year. The IRS requires an S-corp owner-employee who works in the business to be paid a reasonable wage on a W-2 before taking distributions. Underpaying the salary to reduce payroll tax is a top audit trigger.

• Run any missed or catch-up payroll before December 31, since payroll cannot be backdated into a closed year.
• Confirm federal and state payroll deposits and quarterly Form 941 filings are current.
• Prepare W-2s for owner-employees, which are also due January 31.
• Reconcile shareholder distributions and basis so the K-1 is accurate.

Several deductions must be locked in before deadlines, so review them now rather than at filing. Retirement contributions are the largest lever: a solo 401(k) or SEP-IRA lets an owner shelter a significant share of profit, and while SEP contributions can be made up to the extended return deadline, a solo 401(k) needs the plan established by December 31.

• Section 179 and bonus depreciation: equipment and qualifying assets must be purchased and placed in service by December 31 to deduct this year.
• Qualified Business Income (QBI): confirm you are on track for the up-to-20% pass-through deduction and watch the taxable-income thresholds that phase it out for certain service businesses.
• Home office, mileage, and health insurance: gather the records now while the year is fresh.

Yes. A foreign-owned single-member LLC that is treated as disregarded must file Form 5472 attached to a pro forma Form 1120 to report reportable transactions with its foreign owner. This applies even when the LLC owes no US income tax and had minimal activity, including the capital you contributed to start it.

The deadline is April 15, and it moves with the 1120 due date rather than a personal return. The penalty for a late or missing Form 5472 starts at $25,000, so non-resident owners should treat this as the single highest-stakes item on the checklist. Confirm the LLC keeps a separate ledger of every transaction with the owner and any related party.

State filings run on their own calendar, separate from the IRS. Check your state's annual report and franchise tax due dates, since they vary widely: Delaware LLCs owe a $300 franchise tax by June 1, Wyoming runs an annual report on the formation anniversary, and other states set their own dates. Missing them risks late fees and administrative dissolution.

Two more items round out the year. Renew your registered agent so your legal mail and state notices keep arriving, and verify your BOI reporting status is current with FinCEN. Any change in ownership or address during the year may require an updated beneficial ownership report.

Extensions are available for the income tax returns, but they extend time to file, not time to pay. Estimate and pay any balance due by the original deadline to avoid interest and penalties.