Can My Accountant File My Self Assessment and Company Tax Return Together?

This is a question I am asked regularly, usually by directors of small limited companies who wear more than one hat and quite rightly want clarity. In my opinion, it is also a sign that someone is thinking sensibly about their tax affairs rather than treating everything as disconnected tasks.

If you run a limited company and also need to complete a personal Self Assessment tax return, it is very common to assume that these can simply be filed together as one combined submission. From experience, that assumption is understandable, but the reality is a little more nuanced.

The short answer is that your accountant can prepare and manage both your Self Assessment and your company tax return at the same time, but they cannot technically file them together as a single return. They are separate legal filings, governed by different rules, deadlines, and systems at HMRC. However, when handled properly, they should absolutely be coordinated, aligned, and treated as part of one joined up tax picture.

In this article, I will explain how the two returns relate to each other, why they cannot be merged into one filing, how accountants typically handle them together, and why doing so properly can save you tax, time, and stress.

Understanding the Two Different Returns

To understand why this question comes up so often, it helps to step back and look at what each return actually is.

A Self Assessment tax return is your personal tax return. It reports your personal income for the tax year, which runs from 6 April to 5 April. This includes salary, dividends, rental income, interest, and any other taxable income you personally receive.

A company tax return, also known as a CT600, is the company’s corporation tax return. It reports the company’s profits for its accounting period and calculates how much corporation tax the company owes. The accounting period is usually based on the company’s year end, not the personal tax year.

From experience, confusion often arises because directors see the same accountant handling both and assume it is one process. In reality, they are two separate obligations that need to talk to each other.

Why They Cannot Be Filed as One Combined Return

HMRC treats individuals and companies as completely separate taxpayers. Even if you are the sole director and shareholder, the company is its own legal entity.

Self Assessment returns are filed through the personal tax system. Company tax returns are filed through HMRC’s corporation tax system using different software and different authorisations.

In my opinion, this separation is actually helpful, because it keeps personal and business tax liabilities distinct. However, it does mean there is no such thing as a single combined submission that covers both.

That said, the fact they are filed separately does not mean they should be prepared in isolation.

How the Two Returns Are Linked in Practice

Although the filings are separate, the numbers are closely linked.

Your Self Assessment often depends on figures that come from the company accounts and company tax return. Your salary is taken from payroll records. Your dividends are taken from company dividend vouchers. Benefits in kind are linked to company provided benefits. Director loan account movements may also affect your personal tax position.

From experience, preparing a Self Assessment before finalising the company accounts is a recipe for errors. In my opinion, the correct order matters.

The Correct Order of Preparation

In practice, most accountants follow a logical sequence.

First, the company accounts are prepared. These determine the company’s profit, reserves, and ability to pay dividends.

Next, the corporation tax calculation and CT600 are prepared based on those accounts.

Once the company figures are final, the director’s personal income can be confirmed. Salary figures are already known from payroll. Dividends can be confirmed from board minutes and vouchers. Any benefits in kind can be finalised.

Only then is the Self Assessment prepared.

From experience, this approach ensures consistency and avoids situations where dividends are declared personally that the company did not actually have reserves to support.

Can the Accountant Submit Them at the Same Time?

While they cannot be merged into one return, your accountant can absolutely submit them around the same time.

Many firms deliberately align their workflow so that once company accounts are signed off, the corporation tax return and the director’s Self Assessment are both submitted within the same window.

In my opinion, this is good practice. It gives you a clear picture of your overall tax position and avoids nasty surprises months later.

Why Coordination Matters More Than Filing Date

I often tell clients that coordination matters far more than whether returns are submitted on the same day.

If the company tax return shows one set of figures and the Self Assessment shows another, HMRC systems may not immediately spot it, but problems can arise later.

From experience, mismatches often come to light during enquiries, compliance checks, or mortgage applications.

In my opinion, having one accountant oversee both returns reduces the risk of inconsistencies dramatically.

What Happens If Different Accountants Handle Each Return?

Some people use one accountant for the company and another for personal tax. While this is possible, it introduces risk.

From experience, this setup relies heavily on good communication and timely sharing of information. If one side changes a figure and the other is not informed, errors creep in.

In my opinion, this is one of the strongest arguments for having the same accountant or firm handle both, even though the filings remain separate.

Filing Deadlines Are Different

Another reason the returns cannot be treated as one is that the deadlines are different.

Self Assessment returns are due by 31 January following the end of the tax year if filed online.

Company tax returns must be filed within 12 months of the end of the accounting period, but the corporation tax itself is usually payable nine months and one day after the year end.

From experience, this difference in timing catches people out. They assume everything is due at the same time. It is not.

Paying the Tax Is Also Separate

Even if both returns are prepared together, the payments are separate.

Corporation tax is paid by the company from the company bank account.

Self Assessment tax is paid by you personally from your personal funds.

In my opinion, this separation is healthy, but it reinforces why the filings cannot be combined.

How Dividends Tie the Two Together

Dividends are one of the clearest links between company and personal tax.

Dividends are not an expense in the company accounts. They are paid out of post tax profits. This means the company tax position must be known before dividends can be confirmed properly.

Those same dividends then appear on your Self Assessment and are taxed personally.

From experience, errors around dividends are extremely common when returns are not coordinated. Dividends are declared personally that were never properly documented at company level.

In my opinion, this is one of the strongest reasons to treat the two returns as a joined up exercise.

Director’s Loan Accounts and Personal Tax

Director’s loan accounts are another area where coordination is critical.

If you take money out of the company that is not salary or dividends, it goes through the director’s loan account.

Depending on the balance and timing, this can trigger additional corporation tax charges or personal tax consequences.

From experience, failing to reconcile director’s loan accounts before preparing Self Assessment can lead to incorrect reporting or missed liabilities.

Benefits in Kind and P11Ds

Benefits in kind sit at the intersection of company and personal tax.

The company reports benefits on P11Ds and pays Class 1A National Insurance. The director reports the taxable benefit on their Self Assessment.

If these are handled by different people or at different times, inconsistencies arise.

In my opinion, having one accountant oversee the whole picture makes this far easier to manage.

What HMRC Expects to See

HMRC does not require that the same accountant files both returns, but they do expect consistency.

If figures differ without explanation, HMRC may ask questions.

From experience, HMRC enquiries are often triggered not by large numbers, but by inconsistencies.

In my opinion, joined up preparation reduces the likelihood of those questions being asked in the first place.

Can an Accountant Legally Act for Both?

Yes, provided you authorise them.

Your accountant needs separate authorisations to act for you personally and for the company. These are usually handled through HMRC’s agent authorisation process.

Once authorised, they can prepare and submit both returns on your behalf.

From experience, this is standard practice for most small company accountants.

What About Software and Systems?

From a technical perspective, the returns are filed through different systems.

Corporation tax returns are filed using CT600 compatible software.

Self Assessment returns are filed through personal tax software.

Even if the same accountant prepares both, they are submitted separately.

In my opinion, this technical separation is one reason the idea of filing them together persists as a myth.

Is There Any Advantage to Doing Them Together?

There is no technical advantage in terms of HMRC processing, but there is a significant practical advantage.

Preparing them together allows tax planning decisions to be made with the full picture in mind.

For example, adjusting salary levels, timing dividends, or making pension contributions can affect both returns.

From experience, this holistic approach often reduces overall tax.

What Happens If One Is Filed Before the Other?

Sometimes one return must be filed before the other due to deadlines.

This is not a problem as long as the figures are based on final information.

Problems arise when estimates are used and never corrected.

In my opinion, estimates should be avoided wherever possible.

What I Usually Recommend in Practice

In practice, I usually recommend that company accounts and corporation tax are finalised first, followed closely by the director’s Self Assessment.

Even though the filings are separate, they should be treated as part of one process.

From experience, this approach results in fewer errors, clearer understanding, and better planning.

Common Misunderstandings I See

One common misunderstanding is that filing together would somehow speed up HMRC refunds or reduce scrutiny. It does not.

Another is that filing one automatically updates the other. It does not.

In my opinion, understanding these limitations helps set realistic expectations.

What About Multiple Directors or Shareholders?

If a company has multiple directors or shareholders, the same principles apply.

Each individual files their own Self Assessment. The company files one corporation tax return.

From experience, coordination becomes even more important in these cases.

Is It More Expensive to Have Both Done Together?

Not necessarily.

Many accountants offer combined packages for company accounts, corporation tax, and director Self Assessment.

In my opinion, this often represents better value than splitting the work across multiple providers.

So, can your accountant file your Self Assessment and company tax return together?

Not as a single combined submission, no.

However, your accountant can and should prepare them together in a coordinated way that reflects your full financial picture.

From experience, treating them as linked parts of the same process leads to better accuracy, better tax planning, and fewer surprises.

If you run a company and file Self Assessment, I would strongly recommend working with an accountant who understands both sides and manages them as one joined up job, even though HMRC will always receive them as two separate returns.