There is no payroll department in a one-person Shopify or Amazon business, and there does not need to be. How you get money out of the store depends on the entity, and so does what the IRS taxes. The core rule to internalize first: for sole proprietors and LLC owners, you are taxed on what the store earns, not on what you transfer to yourself.
Draws from the business account
If you are a sole proprietor or a single-member LLC, paying yourself is an owner's draw: move money from the business checking account to your personal account. No payroll, no withholding, no W-2. The draw is not a deductible expense of the business, and it is not income to you in itself; it is just you moving your own money between pockets. Take it weekly, monthly, or irregularly; the IRS does not care about the schedule.
What the IRS taxes is net profit: revenue minus cost of goods sold, ad spend, fees, software, and shipping. That profit lands on Schedule C, and it bears ordinary income tax plus 15.3% self-employment tax via Schedule SE, whether you drew out all of it, some of it, or none of it. A store that nets $90,000 and pays its owner $40,000 in draws is taxed on $90,000. This is the trap ecommerce cash flow sets: profit reinvested into more inventory is still fully taxed, even though the cash is sitting on a shelf as product rather than in your account.
Because nothing is withheld from draws, you fund your own taxes through quarterly estimated payments on Form 1040-ES. A workable rhythm: pay yourself a fixed monthly draw you can live on, and route 25% to 30% of profit into a separate tax account before anything else.
Payroll enters with an S corp
Once an LLC elects S corporation status on Form 2553, the rules invert. Owner-operators of an S corp must pay themselves a reasonable W-2 salary for the work they do before taking profit distributions. The salary runs through actual payroll with withholding and payroll taxes; the remaining profit comes out as distributions that avoid the 15.3% self-employment tax. That split is the entire financial point of the election, and the IRS polices the salary side: pay yourself $12,000 while distributing $150,000 from a store you run full time and you are inviting a reclassification.
For a multi-member LLC taxed as a partnership, owners take draws against their share of profit and may receive guaranteed payments, with each member's share reported on a Schedule K-1.
Practical guardrails that apply at every stage: never pay personal expenses straight from the business account, keep the draw cadence boring and documented, and let the tax account fill before the lifestyle account does. The sellers who get in trouble are rarely the ones who paid themselves too much; they are the ones who never separated the money at all.