Yes, Box 9 on the 5498 contains both employer contributions AND employee contributions. However, the amount with the code S in box 12 on the W-2 is only the employee contributions.
The 5498 Instructions say:
Box 9. SIMPLE Contributions
Enter employer contributions(1), including salary deferrals(2), made to a SIMPLE IRA during 2023, including contributions made in 2023 for 2022, but not including contributions made in 2024 for 2023. Trustees and issuers are not responsible for reporting the year for which SIMPLE contributions are made. Do not include contributions to a SIMPLE 401(k) plan. Also include in box 9 contributions to a Roth SIMPLE IRA.
(1) - employer contributions (of course)
(2) - salary deferrals are the employee contributions that were collected by the employer and passed to the IRA along with the employer contributions.
However, the W-2 instructions says for code S in box 12:
Code S—Employee salary reduction contributions under a section 408(p) SIMPLE plan. Show deferrals(1) under a section 408(p) salary reduction SIMPLE retirement account
(1) deferrals is only the employee contributions.
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