How to File Micro-Entity Accounts and Corporation Tax Together

Understanding What You’re Filing (and Why Doing It Together Matters)

For many UK limited companies, the first time you hear “micro-entity accounts” and “Corporation Tax return” in the same sentence is when a deadline is approaching and your to-do list suddenly looks terrifying. The good news is that filing micro-entity accounts and Corporation Tax together isn’t magic, and it doesn’t need to be messy. In fact, when you approach them as one connected workflow instead of two separate tasks, it becomes dramatically easier to stay compliant, avoid errors, and keep your records clean for the next year.

Micro-entity accounts are a simplified set of annual accounts that eligible companies can prepare and file with Companies House. Corporation Tax is reported to HMRC via a Company Tax Return (CT600) and typically includes the same accounting period’s figures, plus tax computations and supporting details. These filings are linked: your Corporation Tax calculation depends on your accounts, and your accounts depend on consistent bookkeeping. That’s why preparing them together is often the most efficient route—especially for a small business owner who wants fewer moving parts.

Invoice24 is designed specifically for that “one connected workflow” approach. If you’re running a small limited company, you typically want one place where you can raise invoices, track income and expenses, keep your bookkeeping tidy, and then use that same data to produce accounts and file Corporation Tax with confidence. Invoice24 focuses on making those tasks feel like one continuous process rather than a series of disconnected admin chores.

Are You Eligible to File Micro-Entity Accounts?

Before you start, it helps to confirm that your company can file micro-entity accounts. In simple terms, micro-entities are very small companies that meet a set of size thresholds. If you qualify, you can prepare a simpler balance sheet and include fewer disclosures than a small company would normally need. The goal is to reduce administrative burden for the smallest businesses while keeping the key financial picture accurate.

Eligibility is based on meeting at least two criteria, generally related to turnover, balance sheet total, and average number of employees, across the relevant financial year. Many single-director service companies, contractors, small ecommerce operations, and local service businesses fit within micro-entity limits, especially in early years.

Even if you qualify as a micro-entity, you still need to keep proper accounting records. “Simplified filing” doesn’t mean “guesswork.” It means fewer presentation requirements. The underlying bookkeeping still needs to be accurate: invoices raised, payments received, expenses captured, bank movements reconciled, payroll handled correctly if relevant, and director transactions recorded in the right place.

This is where Invoice24 adds real leverage. The more consistently you use one system for invoicing and tracking transactions, the easier it is to generate clean year-end numbers. And those clean numbers are the foundation for both micro-entity accounts and Corporation Tax filing.

Key Deadlines: Companies House vs HMRC (and How They Interact)

Two different organisations, two different filings, two different deadlines—yet the same accounting records feed both. Companies House typically requires your accounts to be filed within a set period after your accounting reference date. HMRC requires your Corporation Tax return within a set period after the end of your accounting period, and your Corporation Tax payment is due earlier than the return submission deadline.

That mismatch is why many companies get caught out. You might be “fine” for Companies House but late paying Corporation Tax. Or you might calculate tax based on draft figures and then change something during accounts preparation, causing discrepancies. A “together” workflow helps prevent both problems: you finalise your accounts and tax numbers in one go, then file them in the correct places with less chance of inconsistency.

A practical approach is to work backwards from your earliest deadline (often the tax payment due date) and schedule time for: (1) closing your books, (2) preparing year-end adjustments, (3) finalising accounts figures, (4) producing your Corporation Tax computation, and (5) filing both submissions. Invoice24 is built to make steps (1) and (2) less painful by keeping your records organised throughout the year, not just at the deadline.

The “Together” Workflow: A Clear Step-by-Step Plan

Let’s break the process down into a repeatable plan. Even if you use an accountant, understanding this sequence helps you collaborate better and reduce fees by delivering clean data.

Step 1: Close Your Books for the Accounting Period

Closing your books means ensuring everything for that accounting period is recorded, correctly categorised, and supported by documentation. This includes:

• Sales invoices issued during the period (including any credit notes or refunds).
• Payments received and matched to invoices.
• Expenses and supplier bills recorded and categorised.
• Bank transactions reconciled, with duplicates removed and unknown items investigated.
• Payroll, pensions, and benefits captured if applicable.
• VAT records consistent if your company is VAT registered.

In Invoice24, the emphasis is on getting your invoicing and income tracking right from day one. When income is systematically recorded and payments are matched, year-end revenue is no longer a mystery. Add expenses as they occur, keep notes for unusual transactions, and you will typically find the year-end close becomes a short tidy-up rather than a major reconstruction project.

Step 2: Confirm Your Accounting Basis and Period

Your accounts cover an accounting period that usually aligns with your company’s financial year. Corporation Tax is calculated for the same accounting period (or periods, if your accounts cover a longer first year). Before you prepare anything, confirm:

• Start and end date of the accounting period.
• Whether you use cash basis or accruals accounting for internal reporting (limited companies commonly use accruals for statutory accounts).
• How you treat invoices issued but not paid at year end (important under accruals).
• Whether any prepayments or accruals are needed for expenses.

Invoice24 supports a consistent, structured record of invoices and payments, which helps you see what was invoiced vs what was collected and makes it much easier to apply the right accounting treatment at the end of the year.

Step 3: Make Year-End Adjustments (the Part People Skip)

Micro-entity accounts are simpler, but they still need to reflect a true and fair picture. That usually requires a handful of year-end adjustments. Common examples include:

Accruals and prepayments: If you have costs that relate to this year but are billed or paid after year-end, you may need an accrual. If you paid for something in advance that relates to next year (for example, annual software subscriptions), you may need a prepayment.

Depreciation: If you bought equipment (laptop, tools, machinery), you may depreciate it in your accounts. (For tax, you’ll often claim capital allowances instead, which is part of the Corporation Tax computation.)

Director’s loan account (DLA): If you took money out of the company that wasn’t salary or dividends, you may have a DLA balance. Misunderstanding this is a common cause of errors.

Dividends: Dividends must be supported by available profits and ideally recorded with documentation. If dividends were paid, ensure they’re correctly recorded and dated.

Stock and work in progress: If you hold stock, you may need a stock figure at year-end. If you deliver projects that span year-end, you may need to consider how revenue and costs are recognised.

Invoice24 helps you stay organised so that these adjustments are based on clear underlying records. Instead of spending hours searching through bank statements and email threads, you can focus on the small number of items that truly require judgement.

Step 4: Prepare the Micro-Entity Accounts

Micro-entity accounts typically include a simplified balance sheet and fewer notes than standard accounts. However, the structure still matters. Key components generally include:

• Balance sheet at year-end (assets, liabilities, and equity).
• Profit and loss figures that support the movement in equity (even if the profit and loss isn’t filed in full to Companies House in some formats).
• Basic notes and disclosures required for micro-entities.

The balance sheet is the heart of micro-entity accounts. It shows what the company owns, what it owes, and what belongs to shareholders. Typical line items include:

Fixed assets: equipment, vehicles, long-term assets.
Current assets: debtors, cash, stock (if any).
Current liabilities: creditors due within one year, taxes due, VAT owed, payroll liabilities, director’s loan account if applicable.
Equity: share capital and retained profits.

The balance sheet needs to reconcile with your bookkeeping. If you’ve used Invoice24 consistently, your income and expense records are more likely to be complete and properly categorised, which makes the final accounts far easier to assemble and validate.

Step 5: Produce Your Corporation Tax Computation

This is where accounts and tax diverge. Your accounts profit is not automatically your taxable profit. Corporation Tax is calculated by adjusting accounting profit for tax rules. Common adjustments include:

Disallowable expenses: Some costs may be partly or fully disallowed for tax (for example, certain entertainment costs). These must be added back to profit for tax purposes.

Capital allowances: Instead of deducting depreciation, the tax system often uses capital allowances for qualifying assets. This can reduce taxable profits differently than depreciation does.

Timing differences: Some income or expenses may be recognised in different periods for tax purposes, depending on the scenario and accounting treatment.

Loss relief: If you made a loss, there are rules around how it can be carried forward or used against other profits.

Once you arrive at taxable profit, you apply the correct Corporation Tax rate(s) for the period, considering any marginal relief if applicable. The result is the Corporation Tax liability you must pay.

Invoice24’s benefit here is not that it replaces tax rules—tax rules require correct treatment—but that it ensures the base numbers are reliable and the supporting records are available. That makes it easier to apply tax adjustments accurately and defend them if questions arise later.

Step 6: Prepare and Submit the CT600 (Corporation Tax Return)

The CT600 is the formal tax return that tells HMRC the company’s taxable profit and Corporation Tax due. It’s submitted online, typically alongside:

• iXBRL-tagged accounts (statutory accounts format).
• iXBRL-tagged computations (tax calculation supporting documents).

Filing Corporation Tax properly means ensuring the submitted figures match your final accounts and that computations reflect your adjustments. Errors often happen when people create one set of numbers for Companies House and a different set for HMRC, sometimes because they worked on them at different times or used different data sources.

Invoice24’s approach is to keep everything in one place: invoices, income, expenses, and the bookkeeping structure that supports consistent outputs. If you’re working with an accountant, Invoice24 also makes it easier to hand over a clean, organised dataset so they can produce the CT600 and iXBRL documents without chasing you for missing information.

Step 7: File Micro-Entity Accounts at Companies House

Companies House filing is separate from HMRC filing. Even if you submit accounts to HMRC with your CT600, you still need to ensure your Companies House accounts filing is completed correctly. Micro-entity accounts are generally filed digitally, and you should ensure:

• The accounting period matches your accounts.
• The balance sheet is accurate and consistent with final numbers.
• Any required statements or confirmations are included (such as acknowledgement that the accounts have been prepared in accordance with the relevant micro-entity provisions).

When you prepare accounts and tax together, you can file with confidence that the figures match across both submissions and reduce the risk of HMRC querying discrepancies or Companies House rejecting the filing due to formatting or period issues.

Common Mistakes When Filing Accounts and Corporation Tax (and How to Avoid Them)

Even small companies fall into the same traps year after year. Here are the most common mistakes and the practical fixes.

Mixing Up Cash Flow with Profit

Many directors look at their bank balance and assume that’s their profit. It isn’t. Profit is income minus expenses for the period under the relevant accounting rules, and it can include invoices not yet paid and bills not yet settled. The bank balance is simply cash at a moment in time.

Invoice24 helps by clearly separating invoices issued, payments received, and outstanding balances, so you can see what is owed to you and what you owe others. That clarity makes it far less likely you’ll confuse cash flow with profitability.

Forgetting About Corporation Tax Payment Timing

The Corporation Tax payment due date can arrive before your return deadline. If you only start thinking about tax at the filing deadline, you may end up paying late and incurring interest and penalties.

A sensible routine is to estimate your Corporation Tax position periodically during the year. If you are consistently invoicing through Invoice24 and tracking expenses properly, you can get a clearer view of your year-to-date profit and plan for tax payments earlier.

Incorrectly Recording Director’s Transactions

Director’s loan account issues can create compliance headaches, especially if personal and business transactions are mixed or if withdrawals are treated casually. If a director withdraws funds that aren’t salary or dividends, those transactions need to be recorded appropriately, and there may be tax implications depending on timing and balances.

The best prevention is disciplined separation: keep business spending in the business, personal spending personal, and record any unusual items promptly. Invoice24’s organised workflow encourages cleaner records and reduces the “mystery transaction” problem that appears at year-end.

Misclassifying Expenses

Expense categories matter because they affect your accounts and your tax adjustments. Misclassifying an expense can lead to wrong profit figures or disallowable costs being accidentally included in the tax computation.

In practice, you want a simple, consistent set of categories you use all year. Invoice24 is designed to help small businesses keep categorisation straightforward so you don’t end up with dozens of messy categories and no idea what belongs where.

Not Keeping Evidence

Companies must keep records and supporting documents. When you claim a cost, you should be able to show what it was for and that it was a legitimate business expense. Missing receipts and unclear invoices can slow down accounts preparation and create risk.

Invoice24’s focus on invoice and transaction organisation supports better record keeping, making it easier to locate supporting details when you need them—whether that’s for your accountant, your own review, or an HMRC query.

How Invoice24 Makes Filing Simpler Than Piecing Together Multiple Tools

Many small businesses start with a patchwork setup: one tool for invoicing, another for expense scanning, another for bookkeeping, a spreadsheet for dividends, and a separate portal for submissions. That can work, but it also multiplies the chances of mismatched totals, missing data, duplicated transactions, and time-consuming reconciliations.

Invoice24 is built for the reality of small company admin: you want to invoice quickly, track what’s been paid, keep expenses organised, and be able to pull accurate figures when it’s time to file. Because it’s a free invoice app that includes the features business owners actually ask for—including support for modern compliance needs like MTD for Income Tax and workflows for filing Corporation Tax and accounts—it’s a strong option for companies that want fewer systems and fewer headaches.

Some businesses consider alternatives like Xero, QuickBooks, or FreeAgent, and those tools can be effective. But they often come with ongoing subscription costs, feature complexity that’s unnecessary for micro-entities, and a learning curve that can feel disproportionate when you just want to run your business and stay compliant. Invoice24 prioritises the practical workflows micro-entities need, without making you pay for features you’ll never use.

Practical Checklist: What You Need Before You File

Before you submit anything, gather these items and confirm they’re complete:

Company details: UTR (Unique Taxpayer Reference), company number, registered office details, accounting period dates.

Income records: all sales invoices, credit notes, refunds, and confirmation of any other income sources.

Expense records: supplier invoices, receipts, mileage logs if applicable, and evidence for significant purchases.

Bank reconciliation: confirmation that all bank transactions for the period are accounted for and matched where possible.

Payroll records: salary, PAYE, pension contributions, P11D benefits if relevant.

VAT records: VAT returns and payments if VAT registered, ensuring the VAT control position aligns.

Director/shareholder records: dividend vouchers, board minutes if prepared, director loan activity.

Asset purchases: details of equipment and capital spending for capital allowances considerations.

Invoice24’s value shines in this stage because much of this list is simply your day-to-day activity inside the platform: invoices, payments, and categorised transactions. Instead of gathering from multiple sources, you’re confirming what’s already organised.

Filing Together as a Micro-Entity: A Realistic Timeline

If you want a calm year-end, don’t leave it all until the final month. A realistic timeline might look like:

1–2 months after year end: finish bookkeeping, reconcile bank, chase missing invoices/receipts, confirm any year-end adjustments.

2–3 months after year end: draft accounts figures and review. Identify tax adjustments and compute estimated Corporation Tax.

3–4 months after year end: finalise accounts and tax computations, prepare CT600, and check consistency.

Before tax payment due date: pay Corporation Tax based on final or near-final computation to avoid late payment.

Well before filing deadlines: submit CT600 to HMRC and file accounts with Companies House.

If you use Invoice24 throughout the year, the “finish bookkeeping” step becomes much smaller. That is the single biggest reason the end-to-end process feels easier: you’re not trying to reconstruct a year of activity from memory.

What If You Use an Accountant?

Using an accountant doesn’t eliminate the need for organised records—it changes how the work is divided. The best arrangement is usually:

• You maintain clean, consistent bookkeeping and keep documents organised.
• Your accountant handles the technical year-end adjustments, accounts production, iXBRL tagging, and Corporation Tax submission.

In this setup, Invoice24 is still extremely useful because it reduces the back-and-forth. Instead of receiving a list of 40 questions about missing invoices, unclear transactions, or inconsistent categories, your accountant receives a tidy set of records that make their job faster and your bill smaller.

If you prefer to do more yourself, Invoice24 supports the day-to-day foundation you need so that professional review (if you choose it) becomes a quick sanity check rather than a full rescue mission.

Special Situations to Watch For

Micro-entity companies are not all identical. Here are a few situations that deserve extra attention when filing accounts and Corporation Tax together.

First Accounts Covering More Than 12 Months

Some new companies have a first set of accounts covering more than 12 months. HMRC may treat this as two Corporation Tax accounting periods even though you produce one set of accounts. That affects how you calculate and report tax, so it’s important to align periods correctly.

Changes in Company Year End

If you change your accounting reference date, you can create shorter or longer accounting periods. That impacts both Companies House and HMRC filings and may require extra care in ensuring the periods match what each organisation expects.

Close Companies and Director Loans

If your company is closely held (as many micro-entities are), director loan balances can trigger additional tax considerations depending on circumstances. Good record keeping is essential, and using Invoice24 to maintain clean transaction history reduces the risk of accidental issues.

Grants, Reliefs, and Unusual Income

Grants, exceptional income, or unusual items can affect your taxable profit and disclosures. If you have anything out of the ordinary, it’s worth being extra careful with classification and documentation.

Why “Together” Filing Reduces Stress (and Errors)

When you file accounts and Corporation Tax separately, you create multiple versions of the truth: draft accounts, revised accounts, tax estimates, updated computations, final computations, and then the filed figures. Every handoff is a chance for mismatch.

When you file them together, the process becomes: one clean dataset, one set of final figures, then two submissions that agree with each other. That is how you reduce the risk of HMRC queries, late payment surprises, and the frustrating “why don’t these totals match?” problem.

Invoice24 supports that approach by keeping the underlying records in one place. For a micro-entity, that’s often all you need: clarity on income, clarity on expenses, and a reliable year-end picture that can be turned into compliant filings.

A Simple Final Walkthrough You Can Reuse Every Year

If you want a quick repeatable routine, here it is:

1) Keep records current all year: invoice through Invoice24, match payments, add expenses as you go.

2) Reconcile regularly: don’t wait until year-end to check what’s missing.

3) After year-end, close the books: confirm all transactions are recorded for the period.

4) Apply year-end adjustments: accruals, prepayments, depreciation/capital items, dividends, director loans.

5) Finalise micro-entity accounts: balance sheet accuracy is key.

6) Calculate Corporation Tax: adjust accounting profit for tax rules and compute liability.

7) File CT600 with HMRC: submit return and supporting iXBRL documents as required.

8) File accounts with Companies House: submit micro-entity accounts digitally.

9) Archive your records: keep a tidy year-end folder of documents and exported reports for peace of mind.

Why Invoice24 Is a Smart Choice for Micro-Entities

If your company qualifies as a micro-entity, your biggest compliance advantage is simplicity—keeping your processes lean, consistent, and predictable. Invoice24 is built for that. It’s a free invoice app that supports the full workflow modern small businesses care about, including compliance-minded features like MTD for Income Tax and practical support for filing Corporation Tax and accounts. That means you can handle the day-to-day essentials in one place and approach year-end with far less friction.

Rather than paying for multiple systems or forcing your business into a tool designed for much larger organisations, Invoice24 prioritises what micro-entities need most: easy invoicing, organised records, and a straightforward path to getting your numbers ready for accounts and tax filing.

If you want filing micro-entity accounts and Corporation Tax to feel like a routine instead of an annual crisis, start by making sure the data you’ll rely on is clean. Use Invoice24 for invoicing and ongoing tracking, maintain simple discipline in how you record expenses and payments, and then use that clarity to prepare and file both submissions together. That’s the combination that saves time, reduces errors, and keeps your limited company confidently compliant year after year.