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This thread has been incredibly helpful! I'm dealing with a very similar situation with my web design business. I started as a sole prop, got an EIN for client W9s, then formed an LLC but kept it as a disregarded entity. PayPal required the LLC's EIN for their business account setup, so now I have two EINs just like the OP. Reading through all these responses, it sounds like the consensus is pretty clear - keep using the sole prop EIN on tax forms and W9s, and don't worry about the 1099-K having the different EIN. The explanatory statement approach mentioned by several people here seems like the smart way to handle it. One thing I'm curious about though - has anyone actually had the IRS question or audit them specifically because of this EIN mismatch situation? All the advice here makes sense logically, but I'm wondering if there are any real-world examples of this causing problems down the road, or if it really is as straightforward as everyone is saying. Also, for those who mentioned contacting the IRS directly about this - did you call the general taxpayer assistance line, or is there a specific department that handles business EIN questions?
I haven't personally been audited for this specific EIN mismatch issue, but I can share what I've observed from helping other business owners in similar situations. The IRS seems much more concerned with whether you're reporting all your income accurately rather than minor administrative discrepancies like EIN mismatches on 1099s versus tax returns. That said, the explanatory statement approach really is your best protection. It shows good faith effort to be transparent and helps prevent any confusion if an IRS employee does review your return. I've seen cases where people got automated notices asking about unreported income when they had 1099s with different EINs, but these were easily resolved by referring back to the explanatory statement and showing that the income was indeed reported. For contacting the IRS about EIN questions, I'd recommend starting with the Business & Specialty Tax Line at 1-800-829-4933. They're generally better equipped to handle entity structure questions than the general taxpayer assistance line. Just be prepared for long hold times - that's where services like the Claimyr one mentioned earlier in this thread can actually be helpful for getting through to a live person without spending your entire day on hold. The bottom line is this situation is way more common than you might think, and the IRS systems are designed to handle it as long as you're being consistent and transparent about your reporting.
I've been through this exact same scenario with my consulting LLC and can confirm what others have said here - you're absolutely on the right track with your thinking! The key thing to remember is that even though you're operating as an LLC, the IRS still sees you as a sole proprietor for tax purposes since it's a disregarded entity. So yes, continue using your original sole prop EIN (11-1111111) on your Schedule C and any W9 forms you fill out. When that 1099-K comes in from Square with your LLC's EIN (22-2222222), just report that income on your Schedule C like any other business income. The IRS won't have any issues with this - their systems can cross-reference both EINs to your SSN. I'd definitely echo the advice about including an explanatory statement with your tax return. Something simple like: "Taxpayer operates [LLC Name] as a single-member LLC taxed as a sole proprietorship. Income reported on 1099-K forms under EIN 22-2222222 is included in Schedule C business income reported under EIN 11-1111111." This just gives the IRS a clear paper trail if anyone ever reviews your return. The situation you described with Square requiring the LLC's EIN is super common - payment processors often have strict verification requirements that don't align perfectly with tax reporting rules. But that's totally fine as long as you're consistent on the tax side of things. You're definitely not in a "paperwork mess" - this is actually a pretty standard situation that lots of single-member LLC owners deal with!
This is such a relief to read! I'm actually in the exact same boat - started as sole prop, converted to LLC for protection, but kept it disregarded for taxes. Then Stripe demanded the LLC EIN for merchant services, so now I'm juggling two EINs too. I was losing sleep over whether the 1099-K mismatch would trigger some kind of audit or penalty, but hearing from everyone here that this is totally normal has really put my mind at ease. The explanatory statement approach makes so much sense - it's like leaving a note for the IRS saying "hey, I know this looks weird, but here's what's happening." One quick question though - when you say "consistent on the tax side," does that mean I should NEVER use my LLC's EIN on any tax-related documents? Like what about state tax filings or local business license renewals? Or is this guidance specifically just for federal tax forms like Schedule C and W9s?
Don't stress too much about this! I accidentally selected "retail" for my SAAS business two years ago and it's never caused any issues. The business category on the EIN application isn't as critical as people make it out to be. The IRS cares more about accurate income reporting than the specific category you select during application.
While it might not have caused problems yet, selecting the wrong business category could potentially trigger unnecessary scrutiny during an audit. The IRS might question why a "retail" business is reporting primarily service-based income. Better to get it right from the start!
Great question! I went through this exact same process last year for my SaaS startup. After researching extensively and consulting with my accountant, I selected "Service" for our EIN application. The reasoning is that SaaS businesses are fundamentally providing ongoing access to software functionality rather than selling a tangible product. Even though customers "purchase" subscriptions, what they're really buying is continuous access to your service platform. This puts it squarely in the service category rather than retail, which is typically reserved for businesses selling physical goods or one-time software purchases. The IRS views subscription-based software access as a service offering, similar to how they'd classify other subscription services like consulting or cloud hosting.
Thanks for sharing your experience! This is really helpful to hear from someone who's actually been through the process. Did you run into any complications or questions from the IRS after selecting "Service"? I'm curious if there were any follow-up requirements or if the process was straightforward once you made that selection. Also, how did your accountant help guide you through this decision - did they have specific criteria they used to determine service vs retail for SaaS businesses?
One thing I haven't seen mentioned yet is the importance of documenting your correction process thoroughly. Keep detailed records of every amended return filed, every payment made, and all correspondence with the IRS. This documentation becomes crucial if there are any disputes later or if the IRS has questions about your corrections. Also, consider requesting penalty abatement letters for each tax year once you've filed the corrections and made payments. The IRS sometimes grants relief for reasonable cause, especially when businesses proactively correct mistakes. Your cooperation in fixing this voluntarily could work in your favor. For the partner who was incorrectly paid through payroll, make sure they understand they'll need to file amended individual returns (1040X) for each affected year. The timing matters here - generally you have 3 years from the original due date to amend and claim refunds, so depending on when those original returns were filed, some years might be getting close to that deadline. Finally, once this is all corrected, establish proper ongoing procedures to prevent this from happening again. Set up quarterly partnership meetings to review tax obligations and consider working with a bookkeeper or accountant who understands partnership taxation.
This is excellent advice about documentation! I'm just starting to navigate a similar partnership mess and hadn't thought about the 3-year deadline for amended returns. That's a really important point - some of those earlier years could be running out of time for the partner to claim any refunds they might be owed. One question about the penalty abatement process - do you request that after all the corrections are filed and processed, or can you submit the abatement request along with the amended returns? I'm wondering about the timing since we want to be proactive but don't want to slow down the correction process. Also, when you mention establishing proper procedures going forward, what specific systems would you recommend for a small partnership to stay on top of quarterly obligations? We definitely don't want to end up in this situation again.
Great question about timing! You can actually request penalty abatement at different stages: **Timing Options:** - Submit abatement requests with the amended returns using Form 843 (Claim for Refund) - this can help get everything processed together - Wait until after assessment notices are received, then request abatement - sometimes easier to argue specific penalty amounts this way - Request abatement after making partial payments to show good faith I'd recommend submitting the abatement request along with your amended returns, especially since you're voluntarily correcting. Include a detailed explanation of reasonable cause (reliance on incorrect advice, business complexity, etc.). **For ongoing procedures, here's what works well:** 1. **Quarterly calendar reminders** for estimated tax payments and partnership obligations 2. **Monthly bookkeeping reviews** to catch classification issues early 3. **Annual tax planning meetings** in Q4 to review entity structure and compliance 4. **Professional oversight** - even if just annual CPA review of your processes **Pro tip:** Set up a simple partnership compliance checklist that includes K-1 preparation deadlines, extension filing dates, and state requirements. Many small partnerships fail because they treat it like a simple business structure when it actually has significant ongoing compliance requirements. The key is building systems now while this correction process is fresh in your mind - you'll never want to go through this again!
I went through a very similar situation with my LLC about 18 months ago. We had the same setup - multi-member LLC treated as partnership, but one partner was being paid through payroll for about 3 years while we never filed a single 1065. Here's what I learned from the correction process: **The good news:** The IRS was actually pretty reasonable when we proactively came forward to fix it. We used the Voluntary Classification Settlement Program (VCSP) which significantly reduced our penalties. **The process we followed:** 1. Filed all missing 1065s simultaneously with a detailed cover letter explaining the situation 2. Issued corrected K-1s to the partner who was on payroll 3. Filed amended 941s to remove the partner from payroll 4. The partner filed 1040X returns for each year to report the income correctly **What surprised me:** The partner actually came out ahead in one of the years due to the Section 199A deduction they qualified for as a partner but couldn't claim as an employee. The additional self-employment tax was painful, but the overall tax picture wasn't as bad as we feared. **My advice:** Don't wait any longer to start this process. The penalties keep accruing, and you're getting close to statute of limitations issues for some potential refunds. Also, consider hiring a tax professional who specializes in partnership corrections - it was worth every penny for the peace of mind and to make sure we didn't miss anything. The whole correction took about 8 months to fully resolve, but we were able to set up payment plans for the additional taxes owed. It's definitely stressful, but very fixable!
Great discussion here! I work as a tax preparer and want to emphasize a few key points for anyone in similar situations: 1) Keep ALL receipts and contracts - the IRS may want to see the full paper trail if audited 2) Document the "before" condition - photos of the failing systems can help prove these were necessary improvements, not optional upgrades 3) Consider getting a professional appraisal if your improvements are substantial (over $25K) - this can help establish the added value For the original poster, since you're married filing jointly and this was your primary residence, you're definitely covered by the $500K exclusion. But having proper documentation is still crucial for peace of mind and potential future property sales. One more tip: if you used any financing for these improvements (loans, credit cards, etc.), the interest payments generally can't be added to basis, but the principal amounts can be.
This is incredibly helpful advice! The point about documenting the "before" condition with photos is brilliant - I wish I had thought of that when we were dealing with our failing systems. We definitely have the contracts and receipts, but photo evidence of why the work was necessary would have been great backup. One question about the professional appraisal - is that something you'd recommend getting before or after the improvements are made? We're at $28,500 total which is over your $25K threshold. Would an appraisal help establish the added value even if we don't need it for this particular sale due to the exclusion? Also really appreciate the clarification on financing costs. We did put some of it on a credit card initially, so good to know only the principal counts toward basis, not any interest we paid.
Ideally you'd want to get an appraisal both before and after major improvements, but that's often not practical. For your situation, a post-improvement appraisal could still be valuable - it helps establish the total value added to your property, which strengthens your documentation for the IRS. Even though you don't need it for this sale due to the exclusion, having that professional documentation could be helpful if you ever buy another property and need to establish a pattern of legitimate home improvements. Plus, if you ever convert this to a rental property or face any other tax situations, having rock-solid documentation of the improvements' value is always beneficial. The appraisal doesn't have to be a full formal appraisal either - sometimes a simple letter from a local appraiser stating the estimated value added by the improvements is sufficient and much less expensive than a complete appraisal report.
This thread has been incredibly informative! I'm actually in a very similar situation - we installed a new septic system ($19,000) and upgraded our well pump system ($8,500) about 18 months ago on our primary residence. One thing I wanted to add that I learned from our county health department: they actually keep records of all septic permits and inspections, so even if you've lost some paperwork, you can often get copies of the official documentation from your local permitting office. This was a lifesaver for us when we needed proof that our old system had failed inspection. Also, for anyone dealing with well improvements, check if your state has a well registration database. Many states maintain records of well installations and major repairs that can serve as additional documentation for the IRS. It's reassuring to know that even though most of us probably qualify for the primary residence exclusion, having all this documentation properly organized will be valuable for any future property transactions!
This is such valuable information about getting records from the county! I had no idea they kept those kinds of records that could be accessed later. That's definitely going to save me some stress since I know I'm missing a few pieces of documentation from our well installation. Quick question - when you contacted your county health department, did you need to provide any specific information beyond your property address? I'm wondering if there's a particular department or process for requesting those records. Also, was there any fee involved? The state well registration database is another great tip. I'll definitely look into that for our area. It's amazing how many backup sources of documentation exist that most people (myself included) never think about until they need them!
Effie Alexander
For your truck question - be SUPER careful here. I made a $19k mistake my first year in business by assuming I could just deduct a vehicle purchase 100%. If you're using the vehicle EXCLUSIVELY for business (like, literally never for personal use), you might be able to deduct the full amount under Section 179. But if you use it for personal stuff too (even occasionally), you can only deduct the business-use percentage. Also, SUVs and trucks over 6,000 lbs have different rules than smaller vehicles. Make sure you know which category yours falls into!
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Melissa Lin
ā¢This!! I got audited because I claimed 100% business use on my truck when really it was more like 85%. Had to pay back taxes plus penalties. Not fun.
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Dmitry Ivanov
Hey Vince! Congrats on your business success so far - that's awesome that it's doing better than expected! Just to add to the great advice already shared here: since you're only 4 months in, you're actually in a perfect position to set up good tax habits from the start. The quarterly payment system everyone mentioned is definitely the way to go, and you're not too late to start. For your $26k truck scenario - the key thing is documentation. Keep a detailed log of every business trip (date, destination, business purpose, mileage). If you use it for any personal driving, calculate that percentage because the IRS will want to see those numbers if they ever audit. One more tip that saved me in my first year: open a separate business savings account specifically for taxes. Every time you get paid, immediately transfer 25-30% into that account. It makes quarterly payments so much less stressful when the money is already set aside and earmarked for taxes. You're asking all the right questions - way better to figure this out now than scramble at tax time!
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Amara Torres
ā¢This is such solid advice! The separate tax savings account tip is brilliant - I wish someone had told me that when I was starting out. I'm curious though, is 25-30% typically enough for most small businesses? I've heard some people recommend setting aside even more, especially if you're in a higher income bracket or live in a state with income tax. Also, do you recommend keeping that tax money in a regular savings account or something that earns a bit more interest since you'll be holding it for months at a time?
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