You and the other person are not "partners" in the S corp but are instead shareholders in the S corp. As shareholders, you are both employees of the S corp. Neither of you is self-employed with respect to the S corp and neither of you can independently make contributions to a self-employed retirement plan based on income from the S corp. Any retirement plan contributions based on income from the S corp would have to be made to a retirement plan established by the S corp, with contributions up to the statutory maximums based on each individuals wages reported on the Form W-2 provided to the individual by the S corp. Any SEP contributions must be the same percentage of compensation for all (both) employees. Employer profit-sharing contributions to a 401(k) plan can be subject to anti-discrimination testing, depending on the type of plan. (Unless the other shareholder is your spouse, a 401(k) plan would not be a solo 401(k) plan.) Since you are employees with respect to the S corp, not self-employed, you do not report on your individual tax returns any deduction for retirement contributions to the retirement plan established under the S corp. The deduction is taken on the S corp's tax return.
Additionally, if the other shareholder has separate self-employment income, that shareholder's separate self-employment business and the S corp might be considered a controlled group for the establishment of any retirement plan, depending on the relative proportion of ownership shares involved. All businesses in a controlled group are considered to be a single employer for the purpose of establishing a retirement plan.
If the SEP plan is established with Form 5305-SEP, no plan other than another SEP plan can be maintained by the S corp in the same taxable year. Since most SEP plans are established using Form 5305-SEP, this generally means that the S corp cannot maintain a SEP plan and a 401(k) plan in the same year.
If the S corp establishes a 401(k) plan, the amount that each of you can contribute as elective deferrals or Roth contributions is independent of the other.
