If you run an S-Corporation, your bookkeeping problem is not 'send an invoice.' It is the IRS-mandated tightrope of paying yourself a reasonable W-2 salary, running real payroll with 941s and W-2s, taking the rest as a distribution, and keeping every penny separate from personal money so your corporate veil and your basis schedule both survive an audit. Subscription cloud apps keep raising prices and still nickel-and-dime you for payroll, and most of them quietly assume you are a sole proprietor. FreshLedger Pro is a Windows desktop accounting system built around real double-entry books, owner payroll, MACRS depreciation, and clean K-1-ready reports your CPA can actually use. It is a one-time $799 purchase. We know it works for S-corps because we use it to run a real S-corp's payroll, including quarterly 941 filings and year-end W-2s.
S-Corp owners have a specific list of jobs no consumer accounting tool handles cleanly. Here is how FreshLedger Pro maps to each one. Owner payroll as a real W-2 employee. FreshLedger Pro runs scheduled payroll with federal income tax withholding, Social Security and Medicare (both employee and employer halves), and federal unemployment. It produces the figures you need for Form 941 each quarter, Form 940 annually, and W-2/W-3 at year end. You set the owner's wage, the system computes withholdings using the current-year tables, and the journal entries hit Wages Expense, Payroll Tax Expense, and the related liability accounts automatically. Reasonable compensation tracking. Because FreshLedger Pro is double-entry, owner W-2 wages and shareholder distributions live in different accounts and never get blurred. You can pull a year-to-date wages report next to a distributions report at any time, which is exactly the comparison your CPA wants when defending reasonable comp. Separate books from personal. The S-corp file is its own company file. There is no shared chart of accounts with your personal finances, no accidental commingling, and the equity section is structured for a corporation: Common Stock, Additional Paid-in Capital, Retained Earnings, and Shareholder Distributions. K-1 prep support. At year end you can hand your CPA a trial balance, P&L, balance sheet, and shareholder distribution detail that map directly to Form 1120-S and Schedule K-1 line items. FreshLedger Pro ships a Free Accountant Edition so your CPA can open the file natively, post adjusting journal entries, and hand it back. MACRS depreciation built in. If the S-corp owns vehicles, equipment, or real property, FreshLedger Pro handles full MACRS with the correct conventions and class lives, plus Section 179 and bonus depreciation elections, so fixed assets do not become a December scramble. 1099-NEC for contractors. Vendor payments tagged as 1099-reportable accumulate through the year and print on 1099-NEC at January.
Workflow 1: Semi-monthly owner payroll. You set yourself up as an employee with a 2020+ Form W-4 on file. On the 15th and the last day of each month, you run payroll. FreshLedger Pro calculates gross-to-net: federal income tax withholding using the W-4 method, 6.2% Social Security and 1.45% Medicare withheld from the employee side, and the matching employer 6.2% and 1.45% accrued as employer payroll tax. The net pay posts to a payroll clearing or directly reduces cash; the withholdings sit in liability accounts (Federal Income Tax Payable, FICA Payable, Medicare Payable) until you remit them via EFTPS. When you make the EFTPS payment, you record it against those liabilities and they zero out. At quarter end, the 941 worksheet pulls wages, withheld income tax, and FICA totals straight from those accounts. Workflow 2: Shareholder distribution, done correctly. You decide to take $10,000 out of the business as a distribution, not a paycheck. You write the check (or ACH) from the business account and code it to Shareholder Distributions, an equity account - not to wages, not to owner draws, not to an expense. At year end, that account's balance is the distribution figure that appears on Schedule K-1 line 16 (code D) and reduces your stock basis on your basis worksheet. Because it never touched wages, it does not inflate your reasonable comp and does not get hit with FICA. Workflow 3: Buying a $30,000 truck for the business. You enter the vehicle as a fixed asset, choose the 5-year MACRS class, and pick the half-year convention (or mid-quarter if more than 40% of the year's asset additions land in Q4). You decide whether to take Section 179, bonus depreciation, or straight MACRS, and FreshLedger Pro builds the depreciation schedule for the full recovery period. Each month or year-end, depreciation posts automatically to Depreciation Expense and Accumulated Depreciation. The schedule is the one your CPA needs for Form 4562.
S-Corp accounting has rules sole props never deal with. The IRS requires shareholder-employees who provide services to the corporation to take reasonable compensation as W-2 wages before any distributions - this is the rule behind every reclassification audit in Tax Court. That means real payroll: Form 941 every quarter (lines 2, 3, 5a, 5c for wages, federal income tax withheld, and Social Security/Medicare wages), Form 940 annually for FUTA, Form W-2 and W-3 at year end, and federal deposits on the semi-weekly or monthly schedule the IRS assigns you. At the entity level, the S-corp files Form 1120-S and issues each shareholder a Schedule K-1 (Form 1120-S) showing their share of ordinary business income (line 1), separately stated items like Section 179 (line 11), interest and dividend income, and distributions (line 16, code D). Shareholders track stock basis and debt basis on their own worksheet - distributions in excess of basis become capital gain, so the distribution account in your books has direct tax consequences. Fixed assets follow IRS Pub 946: 5-year property (vehicles, computers, office machinery), 7-year (furniture, most equipment), 15-year (qualified improvement property, land improvements), 27.5-year residential rental, 39-year nonresidential real. Half-year convention is the default; mid-quarter kicks in when Q4 additions exceed 40% of the year's basis; mid-month applies to real property. FreshLedger Pro implements all of these.
FreshLedger Pro is $799 one-time. Payroll tax tables for the current year are included; the optional $99/year update keeps withholding tables current for future years. For a single-owner S-corp running payroll, compare that to subscription stacks: cloud bookkeeping at roughly $30-90/month plus a payroll add-on at $40-80/month plus per-employee fees runs $1,000-$2,000 per year, every year, forever. Over five years the subscription path is $5,000-$10,000; FreshLedger Pro is $799 plus four optional $99 updates - under $1,200 for the same five years, and you can skip an update year if your withholding tables have not materially changed. The Accountant Edition is free for your CPA, so there is no second seat to pay for at tax time.
FreshLedger Pro is not the right tool for every S-corp. If you have multiple shareholders or a bookkeeper who needs to be in the file at the same time as you, the single-user-at-a-time file model will frustrate you. If you want transactions to flow in automatically from your bank, FreshLedger Pro does not have live bank feeds - you download OFX, QFX, QBO, or CSV from your bank's website and import it (usually a 5-minute weekly task, but it is manual). If you work primarily on a Mac or want to approve payroll from your phone, there is no native Mac or mobile app; Mac users run it in a VM. And because it is real double-entry accounting, expect a real learning curve if you are coming from an invoice-only tool.
One-time-purchase accounting software with built-in payroll, full depreciation handling, and a free Accountant Edition for your CPA.
Buy FreshLedger Pro — $799One-time purchase. No subscription. Free Accountant Edition included.