This is a very important study comparing the N budget and N transformations in organic and integrated farming. 15N tracing method is applied and all the components of N-cycling are analysed , both mineral N and gaseous N forms. This very detailed study allows to almost close the N budget which is a very challenging task and authors manage this exceptionally well.

The manuscript is very well prepared, provides the summary of results very clearly, although this is a very complex dataset. I’ve read this manuscript with pleasure and interest, and I definitely support the publication in Biogeosciences. I only have some minor comments which could strengthen some technical aspects of the manuscript and the data discussion. Especially, to enhance your discussion I suggest to keep it quantitative, since you have quantified all the N fluxes you may quantitatively check all of your discussed assumptions (I give examples in the specific comments). I think it is important since your work is very valuable due to tracing and analysing all of the N budget components and, as far as I know, is probably closest to fully close the N budget.

Specific comments:

Title – is very complex and difficult to follow, containing a conclusion, which is discussed in the manuscript, but not fully sure,  I would suggest a simplification and more generalisation, like eg. Comparison of N balance in integrated and organic farming: 15N tracing approach with analysis of all N-compounds (...) -  the title should rather contain a method applied and an aim of the study, not the main conclusion

L32 units are missing for IF (-8 ± 15) – not clear what this values mean

L 34 as above N balance (48 ±14)

L 72-74 “The only method for in-situ measurement of N2 is the 15N gas flux method” – this is not true because also natural abundance isotope analyses of N2O can be used to quantify N2O reduction and hence – calculate the N2 flux (please check: https://bg.copernicus.org/articles/14/711/2017/, https://bg.copernicus.org/articles/17/5513/2020/ ).

The method has of course its limitations, but 15NGF also has (e.g. the high detection limit and short time of possible measurements after tracer application).

L 167-168 It would be good to describe the preparation methodology, which peripheral was used, which masses were measured, what was the detection limit and precision of the measurements. These are very demanding analyses, so these details are necessary.

Please add a citation of the preparation method applied.

L 325 “52% for OF and for IF (35%)” – the bracket should be removed

L 433-443 You discuss the possible N2 flux underestimation as the missing component of your N-balance. It would be interesting to make some estimations with real values to check this theory in practise. Eg. if we assume the 50% of N2 underestimation (as literature data suggest)  will this really be sufficient to close the N budget? Just looking at the fluxes, I think it isn’t. How large should be the N2 flux really to fill the missing budget? Would this amount be realistic?

L 450  “ratio in this study ranged from 0.01 to 1.00”  to 1? Is this a mistake? this would mean no N2, only N2O - I think you do not have such case, N2 flux is always much higher than N2O flux

L 519 – 522 Did you try to extrapolate these N2 and N2O losses? It is possible to try some extrapolation and asses if this could explain the missing 15N? Eg. Assuming theoretical values of eg. half detection limit for the further period (after these losses can be detected) ? Would this be significant in the N budget change?

547 – 549 “reduction of uncertainty for determination of (…), N2 and N2O emission is not in view“ - this is not fully true, because there are some ideas of enhancement of the 15NGF for in situ measurements (see https://link.springer.com/article/10.1007/s00374-024-01806-z ) , so that maybe better sensitivity for N2 can be attained, but with large costs and efforts

I have reviewed the manuscript entitled “Previous integrated or organic farming affects productivity and ecosystem N balance rather than fertilizer ¹⁵N allocation to plants and soil, leaching, or gaseous emissions (NH₃, N₂O, and N₂).” The study is highly relevant and has been very well executed using an elegant and robust methodological approach. Furthermore, the manuscript is clearly written, and the results are carefully analyzed and discussed. Therefore, I consider the manuscript worthy of publication, as it contributes significantly to our understanding of how agricultural management practices shape nitrogen cycling.

Despite a few minor corrections and suggestions (listed below), my main concern lies in the description and interpretation of the management practices, as well as how the experimental design may limit conclusions about the actual effects of those practices.

As I understand it, although two contrasting management histories (organic farming, OF, and integrated farming, IF) are compared, both soils were managed identically during the experimental period (2021–2022). Thus, the study does not directly compare OF and IF, but rather the legacy effects of those systems. Although the authors acknowledge this limitation in the Materials and Methods (Lines 121–122) and in other parts of the manuscript (e.g., title, abstract [Lines 17–18], introduction [Lines 78–81], and conclusions [Line 605]), I believe a more explicit discussion is needed on how the homogenization of management during the experiment may have biased or limited the interpretation of OF and IF impacts on N cycling.

For instance, some observed differences across crop periods may result from the time elapsed since management homogenization. Green rye was evaluated immediately after management unification, while ryegrass was assessed two years later. Additionally, during the experimental phase, no inorganic N fertilizer was applied; only cattle slurry was used, and at high rates (136 kg N ha⁻¹ in 2021 and 151 kg N ha⁻¹ in 2022), similar to conventional IF practices, and notably higher than typical rates in organic systems. This might have masked key differences between the management systems. It is also important to note that legumes were not part of the rotation during the experimental phase, meaning their role can only be inferred as a legacy effect, rather than being directly assessed.

I strongly recommend including a discussion on these aspects to help readers better understand the scope and limitations of the findings related to management system impacts.

Minor Comments:

- L16–17: The role of legumes in crop rotations is not directly evaluated in this study. I suggest removing or rephrasing this part of the abstract.

- L17–20: The lack of prior studies on this specific comparison does not alone justify the study. Consider strengthening the justification by emphasizing the relevance or potential impact of the findings.

- L54 and L93: Use consistent terminology, e.g., “symbiotic N₂ fixation.”

- L79–81: Clarify that the study evaluates the legacy effects of previous management practices, not their current application.

- L88: What does “65618” refer to? Please clarify.

- L95: The phrase explaining integrated farming is redundant and unclear, revise for clarity.

- L97–98: Was there any estimation of nitrogen inputs derived from symbiotic N₂ fixation during the previous management phase? Or at least the legume biomass production.

- L121–122: I recommend explicitly noting the potential biases introduced by management homogenization here.

- L133: Including photographs or diagrams of the experimental setup would improve reader understanding.

- L353–354: “Silage maize” is mentioned twice, please correct.

- L402–403: Clarify “different”, in what sense were they different? Which value was higher?

- L402–413: Discuss how differences across managements and crops could be influenced by the time elapsed since management homogenization. Notably, differences were not observed in the last two crops, possibly due to longer homogenization time.

- L407–411: The high nitrogen dose applied compared to the previously organic system, could have influenced the observed effects. This should be acknowledged.

-L461: “There was no…”

-L476–479: This short paragraph should be more clearly connected to the previous one for better flow.

- L479: As this is a hypothesis, rephrase the sentence to reflect speculative language.

- L599–601: Consider adding a recommendation for future studies to investigate both legacy and contemporary impacts of agricultural management practices.



Despite these considerations, the study is highly valuable and very well executed, and addressing these points would strengthen the clarity and interpretation of the results.