June Tax Checklist for S Corp Owners and 1099 Contractors: What You Need to Do Now
June doesn’t get much attention in the business world. It’s not tax season. It’s not year-end. But for S corporation owners and 1099 contractors, it might be one of the most useful months to reset.
Quiet? Sure. But also—ideal for catching small problems before they become expensive ones.
So if you’re running an S corp or earning non-W2 income, don’t skip this month. Here’s your practical, slightly opinionated, and not-too-perfect checklist.
1. Reevaluate Your S Corp Salary and Payroll Strategy
Let’s start with the big one: your salary.
If you’re actively working in your S corp, you’re required to pay yourself a reasonable salary. That’s not new. But the definition of “reasonable” can shift—especially if your income or job duties have changed in the last six months.
June is a solid midpoint to ask:
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Is my salary still aligned with IRS expectations?
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Have I increased distributions but ignored my W-2 wages?
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Did I just leave last year’s numbers untouched?
If things are off balance, it’s time to adjust. You don’t need to panic, but you also don’t want to drift too far into audit territory.
Need a quick refresher? Here’s how to pay yourself properly from an S corp.
2. Confirm Your June Estimated Tax Payment (Due June 17)
If you’re earning 1099 income—or pulling distributions from your S corp—you already know the drill:
Quarterly estimated taxes are due June 17.
What’s tricky is that Q2 sometimes creeps up quietly. And if your income has shifted at all this year, your original estimates might be outdated.
Ask yourself:
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Did I take on new clients since Q1?
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Has business grown faster than expected?
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Am I underpaying and risking penalties?
Run the numbers again. Adjust your payment if necessary. You can even automate reminders for future quarters while you’re in the zone.
Oh—and if you’re working on multiple income streams, this guide to tax-saving strategies might come in handy.
3. Update Your S Corp Accountable Plan
Still using Venmo for business expenses? June is your second chance to clean that up.
If your S corp reimburses you for:
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Home office costs
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Cell phone bills
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Business travel
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Vehicle mileage
…then you need a written accountable plan.
Without one, those reimbursements could become taxable income. Which means more tax, not less.
If you’ve never created a formal plan before, don’t overthink it. It’s a simple document. And it’s a great excuse to organize your receipts while you’re at it.
While you’re reviewing, consider whether your benefits package includes things like a self-employed health reimbursement strategy. Because if it doesn’t, you might be overpaying for coverage—and missing out on tax perks.
4. Mid-Year Review of Retirement Contributions
No, it’s not December. But that’s exactly the point.
If you wait until the end of the year to fund your SEP-IRA or solo 401(k), you’ll either forget… or rush the math and leave tax savings on the table.
June is the time to step back and ask:
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Am I on track to max out my retirement contributions?
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Do I need to adjust my payroll to increase deferrals?
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Should I consider catch-up contributions?
Here are your 2025 limits:
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Solo 401(k): $23,000 elective deferral + $7,500 catch-up (if over 50)
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SEP IRA: Up to 25% of compensation, capped at $69,000
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Traditional/Roth IRA: $7,000 (+$1,000 catch-up)
Want to go deeper? Look into the mega backdoor Roth strategy while there’s still time to execute it.
5. Run a Mid-Year Tax Planning Session
Here’s where the best S corp owners separate from the reactive ones.
A quick mid-year session with your tax advisor now can:
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Reassess estimated payments
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Check your deduction strategy
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Rebalance salary and distributions
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Spot audit risks before they grow
It doesn’t need to be long. Even 60 minutes could save you thousands—or at least a headache during Q4.
If you’re earning 1099 income or juggling different ventures, this is also a good time to revisit your entity structure and income classification.
6. Clean Up Business Expenses + Reimbursements
Let’s be honest: you’ve probably got a folder—or a shoebox—of receipts from Q1 and Q2. But how many have actually been:
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Categorized?
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Scanned or digitized?
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Linked to reimbursable expenses?
Probably not all.
Use June to tidy up:
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Travel logs
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Business meals
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Continuing education expenses
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Conferences or medical seminars
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Software or subscription fees
Not sure what qualifies? You might be surprised by the scope of deductible business expenses.
7. Review Your State-Level Tax Exposure
If you live—or work—in a high-tax state like California or New York, June is your wake-up call.
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Are you paying taxes in multiple states?
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Working remotely while your entity is registered elsewhere?
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Thinking of moving?
Each scenario has its own set of tax implications.
Start looking into state-specific strategies to reduce exposure. You might explore residency planning, or dig into how high state taxes affect retirement and relocation.
It’s also a good time to verify that your state-level S corp filings are current. Some states require franchise tax, others don’t. Some charge penalties for missing an annual statement by one day.
8. Explore Advanced Planning: Private Insurance or Captive Models
This isn’t for everyone, but for high-income earners and successful businesses, June could be your intro to alternative strategies like:
These offer risk protection and tax deferral for businesses with excess reserves and long-term planning needs.
They take time to evaluate, though. You can’t set one up overnight in December.
9. Revisit Your Business Entity Setup
Let’s say your income has grown this year.
That’s great—but does your business structure still fit?
Some things to explore in June:
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Should I add a C corp for better income splitting?
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Is my current state of registration still the best choice?
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Should I restructure to accommodate new revenue streams?
If you’re thinking about selling your business, even down the road, this is also a good time to look at how to minimize taxes when selling.
10. Quick Wins to Clean House Before Q3
A few last small tasks that help you stay ahead:
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Collect updated W-9s from contractors
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Renew any expiring business licenses
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Back up accounting software
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Archive bank statements or payroll reports
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Reconcile bank accounts and credit cards
You could probably do these in under two hours. But pushing them to October? That’s how they turn into problems.
Final Thought: Don’t Let “Mid-Year” Fool You
It’s easy to feel like June doesn’t matter much. But it does.
It’s the perfect window between spring tax season and the fall business ramp-up. Things are calm. There’s space to think clearly. That won’t last.
Even if you don’t tackle everything on this checklist, pick two or three items. Adjust your payroll. Clean up your receipts. Book a planning call.
Small moves now can save real money later. And the stress you don’t feel in December? That’s the real win.
FAQ: June Tax Questions for S Corps and 1099 Filers
When are estimated taxes due in June 2025?
The Q2 estimated tax deadline is Monday, June 17, 2025.
Do I need to update my salary mid-year as an S corp owner?
If your role or business income has changed significantly, yes. It’s better to adjust now than risk IRS penalties later.
Can I set up an accountable plan mid-year?
Yes, absolutely. Start it now and document reimbursements properly going forward.
Is it too early to make retirement contributions in June?
Not at all. In fact, it’s ideal. Spacing out contributions avoids cash-flow pressure at year-end.
How do I know if I’m underpaying estimated taxes?
Compare your projected annual income to your current payments. If there’s a gap, update your Q2 payment before June 17.
What’s the benefit of a mid-year review?
You get a chance to course-correct—on taxes, salary, deductions—while there’s still time to act.
Do I need to worry about state taxes as an S corp?
Yes, especially if you live or operate in high-tax states, or work across state lines.
Is now a good time to explore captive insurance?
Yes, but only if your revenue supports it. Captives take time to analyze and set up correctly, so June gives you room to explore without rushing.
Visit contact physiciantaxsolutions.com to schedule a consultation and learn how we can help you take control of your tax strategy today.
This post serves solely for informational purposes and should not be construed as legal, business, or tax advice. Individuals should seek guidance from their attorney, business advisor, or tax advisor regarding the matters discussed herein. physiciantaxsolutions.com assumes no responsibility for actions taken based on the information provided in this post.