How does a SEP IRA to Roth conversion work with after-tax funds?

So here’s the story: I put money into my SEP IRA about 5-10 years ago, but my CPA never listed it on my tax returns. I missed that detail too. My CPA is now retired.

The SEP funds are after-tax and never got reported to the IRS. Now, I’d like to convert this SEP IRA to a Roth IRA with a backdoor transfer.

My SEP has actually lost value over the years. For example, I originally deposited $50,000, but it’s now worth $30,000.

If I convert the SEP to a Roth, will it be a taxable event, or is it more like a straight conversion?

Yes, converting will be a taxable event.

To get any benefit, you’d need to amend previous tax years to include the SEP deduction, but those years are probably too old to get a refund. Unfortunately, it means you’d likely get taxed twice here because you didn’t catch the mistake on your original returns (an easy mistake to make if you trusted your CPA).

@Marvin2
That’s what I thought too, but I haven’t actually seen anyone do this before, so I wasn’t completely sure.

Tough mistake for them to make.

@Marvin2
I think my question might not have been clear. The amounts that went into the SEP were never deducted on taxes, so I already paid tax on the whole amount in the SEP account.

My understanding is that after-tax dollars (from the SEP) going into another after-tax account (Roth) would be tax-free, except for any dividends or growth. Or maybe that doesn’t account for any losses in the SEP.

@Azar
Unfortunately, it doesn’t work that way.

Even if you didn’t deduct it in past returns, any withdrawal or conversion from a SEP is still taxed.

Great question… hoping someone with real experience on this will chime in.

Have you been filing Form 8606 with your returns? And do you have any other IRAs?

If your IRAs are all after-tax money, the Roth conversion could be tax-free.

Taryn said:
Have you been filing Form 8606 with your returns? And do you have any other IRAs?

If your IRAs are all after-tax money, the Roth conversion could be tax-free.

Form 8606 is for traditional IRAs only, if I remember correctly. This isn’t a traditional IRA; it’s a SEP, which works a bit differently.

Plus, you couldn’t do after-tax contributions in a SEP back then (you can do Roth SEP now in 2023).

I’m hoping someone who’s more familiar can confirm. I’ve never had a client who skipped the SEP deduction, so I’m not sure how it’s treated, but I think it’s going to be handled as if everything was pre-tax.

Taryn said:
Have you been filing Form 8606 with your returns? And do you have any other IRAs?

If your IRAs are all after-tax money, the Roth conversion could be tax-free.

Since OP is talking about SEP contributions, it’s unclear if these can be treated the same as regular nondeductible contributions. Section 408(o) isn’t directly related since it refers to standard IRA limits.

@Tatum
Maybe they should first roll the SEP into a regular IRA and report the basis, then convert to Roth next year.

Taryn said:
@Tatum
Maybe they should first roll the SEP into a regular IRA and report the basis, then convert to Roth next year.

I don’t think that’s allowed. After-tax SEP contributions weren’t permitted back when they contributed, so rolling it over won’t change that. They might need to treat it as pre-tax regardless. But I’m not certain. OP should really get advice from someone familiar with SEP IRAs.

Taryn said:
Have you been filing Form 8606 with your returns? And do you have any other IRAs?

If your IRAs are all after-tax money, the Roth conversion could be tax-free.

Nope, never filed an 8606. Checked my old returns, and none of them included it.

@Azar
You wouldn’t have. Ignore the 8606 mention—it doesn’t apply to SEP contributions.

Just curious, how did you calculate your contributions for those years? Usually, an accountant gives you a set amount you’re allowed to put in.

@Murray
Yep, my accountant would just tell me, “you can deposit X amount,” and I’d follow that.

Azar said:
@Murray
Yep, my accountant would just tell me, “you can deposit X amount,” and I’d follow that.

And you didn’t take the deduction? That’s hard to believe. Are you totally sure?

Azar said:
@Murray
Yep, my accountant would just tell me, “you can deposit X amount,” and I’d follow that.

The deduction wouldn’t be on Schedule C. It’d be on Schedule 1. Did you check there?

@Murray
Yes, I’m positive. I know it was ultimately my responsibility to double-check.
Just trying to see if I can minimize any tax hit.

Would it maybe be better to just leave the SEP alone and deal with taxes when I eventually take distributions?

@Azar
That’s a personal choice. If you have a low income now, you might convert it and pay the tax at a lower rate. Another option is to roll it into a 401k if your employer allows it, but that only makes sense if you need or want to do backdoor Roth contributions.

Taryn said:
Have you been filing Form 8606 with your returns? And do you have any other IRAs?

If your IRAs are all after-tax money, the Roth conversion could be tax-free.

There isn’t such a thing as a nondeductible SEP contribution.

@Marvin2
That’s what I thought too. Though now, starting in 2023, there is such a thing. But back 5-10 years ago, this didn’t exist.