Your second CPA is correct.
You are an employee of your S-Corp and the S-Corp's maximum contribution to your SEP-IRA is the lesser of 25% of your remuneration or $63.000 for 2023 ($61,000 for 2022). In your case, it would be 25% of $12,500 or $3,125.
Please read this IRS document for more information.
Your first CPA was applying the rules for a self-employed individual which apply for a sole proprietor or a working partner in a partnership or limited liability company.
Please read this IRS document for self-employed individuals.
Your S-Corp has made excess contributions to your SEP-IRA in the past. To correct this, please follow the instructions in this IRS document.
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