Contribution Limits. You can only contribute to your SEP IRA for the previous year if you haven't already maxed out your contributions. For employee contributions, the limit is the same as the traditional and Roth IRA limits -- $5,500 if you're under 50 and $6,500 if you're 50 and older as of 2013.For example, if you've already put in $6,500 in your Roth IRA, you can't add any more to your SEP IRA as an employee.he employer contributions are made with pre-tax dollars while the employee contributions are treated as if the contributions were made to a traditional IRA. Whether you can contribute for a previous year depends on your filing deadlines and how much you've already contributed.