The year 2026 doesn't promise a wave of spectacular "briefcase-laden" audits. Something much more important is changing: the way taxpayers are selected and the scope of the tax authorities' interest . The tax administration is increasingly relying on data, analytics, and automated comparisons.
In practice, this means that inspections in 2026 will be shorter, more precise, and focused on specific risk areas. Below are the most important ones.
Data from systems, not "random checks"
The fundamental change is that inspections increasingly rarely begin with a visit to the company's headquarters. In 2026, they often begin earlier – in the administration's IT systems.
The tax office analyzes data from invoices, records, SAF-T files, declarations, and electronically transmitted information. The audit is based on a signal, not a random selection. This means the office usually already knows what it's looking for before contacting the company.
KSeF – invoicing consistency and process behavior
One of the main areas of interest will be data from the National e-Invoice System. The tax authorities will not only look at individual invoices, but also at patterns of behavior .
In practice, the following will be under scrutiny:
-
differences between the moment of sale and the issuance of the invoice,
-
frequent corrections, especially during specific periods,
-
non-standard use of offline and emergency modes,
-
inconsistencies between invoices and VAT and JPK records,
-
lack of consistency in numbering, dates or transaction patterns.
In 2026, it is not yet about KSeF penalties, but about identifying taxpayers whose processes are not stable.
JPK and accounting books – data quality, not just formal compliance
Another area is accounting data reported in SAF-T structures. The tax authorities are increasingly analyzing them from a logical and comparative perspective.
Particular attention is paid to:
-
inconsistencies between VAT records and accounting books,
-
unusual postings in cost and revenue accounts,
-
lack of clear descriptions of economic events,
-
differences between accounting policy and actual accounting practice.
In 2026, control often comes down to the question: does the data “tell a coherent story?”
Estonian CIT – formalities as a flashpoint
Companies subject to Estonian corporate income tax are of particular concern. Not because the system is flawed, but because the risks are primarily formal .
In practice, the authorities check:
-
timeliness and accuracy of financial reports,
-
completeness of signatures of authorized persons,
-
compliance of the conditions of application of Estonian CIT with the actual structure of the company,
-
moments of payments, benefits to shareholders and transactions with related entities.
In 2026, the tax authorities often return to the question: does the company actually meet the conditions for the lump sum tax or has it only formally chosen it?
Transactions with related parties
Transfer pricing remains one of the most challenging areas for inspection. In 2026, authorities will focus not only on documentation but also on the economics of the transaction.
Particular attention is paid to:
-
intangible and management services,
-
re-invoicing costs without clear calculation,
-
intra-group financing,
-
discrepancies between the agreements and the actual course of the transaction.
Lack of documentation is a problem today, but documentation detached from operational realities is an even greater risk.
Tax losses and low profitability
Companies showing losses or very low profitability are a natural area of interest for the tax authorities, especially when:
-
the loss repeats itself for several years,
-
revenues are growing but results are not,
-
the cost structure differs from that typical for the industry.
In 2026, audits in this area will often be combined with an analysis of the minimum CIT and the feasibility of the business model.
Document circulation and response to letters
More and more often, not only taxes are the subject of inspections, but also the company's reaction to the authorities' actions .
The tax office draws attention to:
-
timely responses to letters,
-
completeness of the explanations provided,
-
consistency of information submitted through various channels,
-
organization of document circulation and internal responsibility.
In the era of e-Delivery, the argument "the letter did not arrive" no longer applies.
What does the tax office expect in 2026?
From the perspective of organ practice, one thing can be said:
In 2026, the tax office expects the company to have mastered the processes , not just correctly submitted declarations.
What is most often questioned is not individual errors, but rather the lack of control over the whole.
How to prepare your company for the 2026 inspections?
The best way is not to “put out the fire”, but to put things in order:
-
invoicing and correction processes,
-
consistency of accounting data,
-
Estonian CIT formalities,
-
rules for document circulation and communication with the office,
-
internal responsibility for taxes.
Grażyna Janowicz, a tax advisor and certified auditor, supports companies in preparing for tax audits in the new, digital world. Consultations and training focus on tax authorities' practices, real-world risks, and implementing solutions that work beyond just "on paper."