2 February 2026

How Self-Directed IRA Custodians Differ From Brokerages

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You might have heard the term self-directed IRA (individual retirement account) before. In recent years, self-directed IRAs have become more popular. In fact, in my work with a self-directed IRA custodian, they are talked about so frequently now that some people believe these are a special kind of IRA. In reality, “self-directed” is a descriptive term that describes who makes the investment decisions inside the plan.

There are four types of IRAs: traditional, Roth, simplified employee pension (SEP) and SIMPLE. Any of the four can be “self-directed.” You can have a “self-directed” IRA at a large brokerage firm where you pick out stocks, bonds or mutual funds. However, your accounts at a brokerage house aren’t truly self-directed because brokerages generally limit investments to the products they sell. A truly self-directed IRA custodian doesn’t sell investments and therefore doesn’t put limitations on one’s investment decisions — other than those imposed by the IRS. So, why don’t traditional brokerages typically allow for self-direction?

Sources Of Revenue 

Much of a brokerage’s revenue is tied to the investments it sells. While commissions have gone by the wayside (for the most part) on individual stock purchases, this is not the case in the qualified plan world (meaning 401[k], 403[b] and 457 plans, etc.) where management fees exist and can be considerable. Furthermore, many investments in the brokerage world have management fees built into the investment itself (i.e., mutual funds). Brokerages have no financial incentive to allow investors to buy alternative investments, such as real estate, notes and private placements.

Administrative Burdens 

Even if a brokerage decided it could price a fee on purchasing an alternative asset, there are administrative burdens to consider. Brokerages allow clients to buy their own assets with a click of a button. Facilitating manual transactions requires more staff and time. As an example, a self-directed custodian assisting a client with owning real estate in their IRA has to deal with closing dates, wires, deeds, title insurance, rent, evictions and property taxes. These are labor-intensive jobs requiring knowledgeable staff. It isn’t an easy transition for large firms that specialize in more straightforward transactions.

Fair Market Valuations 

One responsibility every IRA custodian has is reporting the end of year fair market value (FMV) to the IRS on Form 5498 on an annual basis. This is easy for a brokerage, because its systems provide second-by-second market values. But how would it value a private LLC investment located in Costa Rica? That would be more difficult. Self-directed custodians have agreements with their clients that require clients to provide substantiating documentation of the investments held within their plan. This would require them to reach out to clients for this information, which is another administrative burden. Gathering this data and then the labor-intensive entry of this data is a lot of work.

Differences In Business Models 

So now you know why brokerages do not typically custody “self-directed” alternative assets; let’s talk a little about the differences in the business model of brokerages and self-directed custodians. In other words, what are you paying for?

There are multiple ways a custodian can generate enough revenue to run its business. Brokerages generate much of their revenue through commissions, management and/or advisory fees, which help cover the cost of IRA administrative services. Self-directed IRA custodians don’t sell investments or act as a bank and make loans. They are not fiduciaries and do not provide investment, legal or tax advice. Their only source of income is administrative fees for the manual processing of investment transactions that occur inside accounts.

The bottom line is every financial product comes at a cost. The IRS requires that a third party administer all retirement plans. Unless that third party has alternate ways to generate revenue on your IRA funds, administrative fees are inevitable. You can assume you will be paying some of your hard-earned money in either administration fees (self-directed IRAs) or commissions/advisory fees (brokerages). Which option you choose ultimately depends on your investment needs and goals.

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