Compliance Calendar and Filings the Bookkeeper Manages

• Build and maintain an annual compliance calendar for employment tax returns (Forms 941/944 quarterly or annually, Form 940 annually) and W‑2/W‑3 filing by January 31, plus any required Form 1099 filings (e.g., 1099‑NEC due January 31; 1099‑MISC generally due February 28 or March 31 if e‑filed). Timely deposits and filings are critical to avoid penalties Employment tax due dates | IRS; Instructions for Forms 1099‑MISC and 1099‑NEC | IRS.

• Track and meet the Form 1120‑S filing deadline (generally the 15th day of the 3rd month after year end) and e‑file when required (10+ returns in the calendar year triggers mandatory e‑file). Coordinate with your tax preparer on assembling the return and Schedules K‑1 for shareholders 2024 Instructions for Form 1120‑S | IRS.

Payroll and Reasonable Compensation Administration

• Set up and run officer and employee payroll consistent with the IRS’s position that corporate officers are employees and must be paid reasonable compensation subject to withholding and employment taxes. Ensure employees/officers are on payroll, wages are recorded properly, and withholding/deposits are made on time Employment tax due dates | IRS.

• Manage payroll tax deposits and filings:

  • Determine monthly vs. semiweekly deposit schedules and apply the “$100,000 next‑day” deposit rule if triggered Employment tax due dates | IRS.

  • File Forms 941 (or 944 if eligible), 940 (FUTA), and furnish/file Forms W‑2/W‑3 by January 31; maintain proof of electronic filing and deposits (EFTPS) Employment tax due dates | IRS.

• Book and reconcile payroll to the general ledger; ensure taxable wages include any taxable fringe benefits and that non‑taxable fringes are handled under accountable plan rules Publication 5137, Fringe Benefit Guide | IRS.

Independent Contractors and Information Reporting (Forms 1099)

• Identify nonemployee payees and evaluate whether payments meet information reporting thresholds (e.g., $600 for nonemployee compensation on 1099‑NEC; medical/health care payments on 1099‑MISC; certain gross proceeds to attorneys). Collect W‑9s, track payments, and file required forms by the due dates Instructions for Forms 1099‑MISC and 1099‑NEC | IRS.

• Distinguish employees from contractors—do not “designate” someone by issuing a 1099 instead of a W‑2; misclassification creates payroll tax exposure. Officers performing services must be on payroll; follow employment tax guidance Employment tax due dates | IRS.

Owner Distributions, Loans, and Basis Tracking (Shareholder‑Specific)

• Track all shareholder distributions, contributions, loans to/from the S‑Corp, and repayments. Maintain clear documentation for any bona fide shareholder loans (terms, interest, repayment) to support debt basis if applicable; mere guarantees do not create shareholder debt basis unless the shareholder makes payments S corporation stock and debt basis | IRS; 26 CFR § 1.1366‑2 | eCFR.

• Maintain shareholder stock basis and debt basis schedules annually. Basis increases with pass‑through income and certain items and decreases with losses, nondeductible expenses, and non‑dividend distributions; ordering rules and annual timing are specific 26 CFR § 1.1367‑1 | eCFR; S corporation stock and debt basis | IRS.

• Track and categorize distributions under S‑Corp distribution rules. Maintain the accumulated adjustments account (AAA), earnings and profits (if any), and apply ordering rules to determine whether a distribution reduces basis, is a taxable dividend (if E&P exists), or triggers gain 26 CFR § 1.1368‑1 | eCFR; 26 CFR § 1.1368‑2 | eCFR; IRC § 1368 | U.S. Code.

Accountable Plans, Reimbursements, and Fringe Benefits

• Implement and administer an accountable plan for reimbursing business expenses (mileage, travel, supplies) to employees/shareholders. Under an accountable plan, substantiated business reimbursements are excluded from wages; under a nonaccountable plan, amounts are taxable wages. Maintain policies, capture receipts/per diem logs, and ensure timely substantiation and excess return Publication 5137 | IRS; Publication 463, Travel, Gift, and Car Expenses | IRS.

• Track and report taxable fringe benefits (e.g., personal use of employer‑provided vehicles) in wages, and handle permitted nontaxable fringes under the correct exclusion provisions. Proper valuation and reporting must appear on payroll and W‑2s Publication 5137 | IRS; Publication 15‑B (2025) | IRS.

Fixed Assets, Capitalization Policy, and Depreciation

• Maintain a fixed asset subledger and capitalization policy; record acquisitions with proper classification (land vs. building vs. improvements vs. equipment) and compute depreciation under MACRS, recognizing that land is non‑depreciable and real property is depreciated over longer lives Publication 946 | IRS.

• Prepare annual depreciation schedules and reconcile them to Form 4562 and the tax return; administer Section 179 elections and any special depreciation allowances per current limits 2024 Instructions for Form 4562 | IRS; Publication 946 | IRS.

Banking, Reconciliations, and Monthly Close

• Perform monthly reconciliations of bank, credit card, and payroll clearing accounts; maintain internal controls over cash receipts and disbursements; and retain records to support all entries Publication 542, Corporations | IRS.

• Close the books monthly/quarterly and produce Profit & Loss, Balance Sheet, and trial balances. These financials feed Form 1120‑S schedules (e.g., Schedule L balance sheets; M‑1 reconciling book vs. tax) and K‑1 allocations 2024 Instructions for Form 1120‑S | IRS; 2024 Form 1120‑S | IRS.

Year‑End Tax Package for Form 1120‑S and Schedules K‑1

• Deliver a complete year‑end tax package to the preparer (ledger, trial balance, depreciation schedules, AAA and basis schedules, distribution detail, payroll reports, bank statements, 1099 and W‑2 filings). Accurate books reduce errors on the corporate return and K‑1s furnished to shareholders 2024 Instructions for Form 1120‑S | IRS.

• Coordinate e‑filing of the corporate return when required (10+ returns threshold) and timely furnish Schedules K‑1 to shareholders so they can file their individual returns properly 2024 Instructions for Form 1120‑S | IRS; S corporations | IRS.

Documentation and Recordkeeping

• Establish and enforce a document retention policy covering payroll, W‑2/W‑3/941/940 filings, 1099s, bank statements, invoices, receipts, fixed asset records, shareholder loan notes, and basis/distribution schedules Publication 542 | IRS.

• Retain the underlying support for expense reimbursements (accountable plan) and fringe benefit valuations; ensure timely substantiation and proper payroll inclusion/exclusion Publication 5137 | IRS.

Penalty Awareness and Electronic Payments

• Monitor and minimize exposure to penalties for late filing, late payment, or deposit failures by using EFTPS and calendaring due dates. Timely deposits and filings prevent trust‑fund and other penalties Publication 542 | IRS; Employment tax due dates | IRS.

Why These Bookkeeping Tasks Matter for S‑Corp Owners

• S‑Corps are pass‑throughs with corporate filing responsibilities; payroll must run correctly for officers, information returns must be filed, and distributions/basis must be tracked or owners risk incorrect taxation of losses and cash distributions S corporations | IRS; S corporation stock and debt basis | IRS; 26 CFR § 1.1368‑1 | eCFR.

• High‑quality books reduce preparation time and errors on Form 1120‑S, Schedules K‑1, W‑2/1099 filings, and support positions in case of IRS inquiries. Accurate fixed asset and depreciation records, payroll reporting, and basis schedules are indispensable to claiming the right deductions and reporting the right income 2024 Instructions for Form 1120‑S | IRS; Publication 946 | IRS; Publication 5137 | IRS.

Bottom Line

A good bookkeeper for an S‑Corp owner does far more than code transactions—they run payroll and compliance on schedule, file W‑2s and 1099s, track shareholder basis, loans, and distributions, maintain accountable plan and fringe benefit reporting, manage fixed assets and depreciation, reconcile the books monthly, and deliver complete year‑end packages for Form 1120‑S and K‑1s. These tasks align directly with IRS requirements and keep your S‑Corp audit‑ready while maximizing tax accuracy for the owners. See: S corporations | IRS; Employment tax due dates | IRS; Instructions for Forms 1099‑MISC and 1099‑NEC | IRS; S corporation stock and debt basis | IRS; 26 CFR § 1.1368‑1 | eCFR; 2024 Instructions for Form 1120‑S | IRS; Publication 5137 | IRS; Publication 946 | IRS; 2024 Instructions for Form 4562 | IRS.