This paper presents a methodology to quantify uncertainties in the CAMS-REG European emission inventory, providing both country-level and gridded uncertainty estimates for greenhouse gases and air pollutants to support inverse modelling and emission verification.

The paper is interesting, well written, and cover a much needed aspect of emission inventories preparation.

However, I have some points I would like to see covered and improved before possible publication

- Table 1: why is this table only available for CO2 and CH4? Could you extend this to cover also air pollutants?

- Table 2: please better explain how these values are derived

- section 2.3. I re-read few times this section, but I have to say it's quite complex, and I would like to see this improved, for better clarity. I.e., could you describe the steps in a workflow/graph? There are some efforts in this direction (as Figure 2) but this section 2.3 should be improved, as it is the core of the paper, and at the moment is quite complex to follow

- similar to section 2.3, also section 2.4 should be improved, for better clarity

- Figure 2: also I found this Figure complex, and I cannot easily link it to the rest of the text...could you please improve its readability?

- Table 3 shows optimized and non-optimized uncertainties. To my knowledge, the optimized uncertainties values you get are quite low...are these values strongly affected by the uncertainties values you use as input, and if yes, did you implement a proper sensitivity analysis? Also, as these optimized values are quite small...are there other uncertainty source that should be considered and are not considered in your modelling, to fully define emission uncertainties? please specify

- Section 5 (data availability)... I checked the provided data...I think, to facilitate their use, on top of the usual CAMS-REG format for the data, one should provide a gridded uncertainty data (or at least a python code to convert the CAMS-REG format to a more simple gridded uncertainties field).

The manuscript is very well written, clear, concise, and interesting to read, and the resulting uncertainty estimates for gridded CAMS-REG emission inventories represent a useful and relevant product for the community.

I provide below a few general comments and suggestions that I hope will help further strengthen the manuscript.

General comments

• The manuscript would benefit from a clearer explanation of how the present work relates to preceding studies. Which assumptions are retained across versions, and which have been modified? A concise overview table or a dediacated section could be helpful in clarifying these differences.
• For users familiar with previous versions, a more direct one-to-one comparison would also be valuable. In particular, it would be interesting to understand how the estimated uncertainties are affected by the differences in the approaches between versions.
• The optimization approach plays a central role in "correcting" the prior gridded uncertainties. While I consider the approach itself to be sound and innovative, it may carry a risk of compensating, in some cases, for errors or biases in the prior gridded uncertainty data. It would be useful if the authors could reflect on this potential limitation in the discussion section.

Specific comments

• The authors might consider complementing the boxplots with violin plots. This would provide additional information on the shape of the distributions, including skewness or potential multimodality. This would be particularly interesting for Figure 4, where the boxplots for several sectors appear to be rather skewed.
• Table 3 is not fully clear and is not discussed in sufficient detail in the text. On first reading, I was confused because I assumed that the two columns referred to the same set of countries, and therefore wondered why the non-optimized CO2 values were higher than the optimized values, even though Figure 6 shows scaling factors mostly below 1. However, if I understand correctly, the two columns refer to distinct groups of countries. This should be clarified in the table caption and/or the main text.
• Figure 5: I find the logarithmic colour scale, especially for the relative uncertainties, somewhat difficult to read. Adding more tick labels could improve readability, for example at 0.2, 0.4, ....

Technical corrections

• add hyperlinks to references
• Line 358 typo: if -> is