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The phrase "although the difference was not substantial" is correct and usable in written English.
You can use it when discussing a comparison or contrast where the difference between two items or situations is minimal or insignificant.
Example: "The two products were similar in many ways, although the difference was not substantial in terms of performance."
Alternatives: "even though the difference was minor" or "despite the negligible difference".
Exact(1)
Primary bubonic plague case-patients more often received effective antibiotics, although the difference was not substantial (bubonic 89%; septicemic 81%; pneumonic 79%).
Similar(58)
Of those who agree that there is not much evidence against evolution, most do not think it is controlled by God, although the difference is not substantial.
However, the difference is not substantial.
Nonetheless, the difference is not substantial in this case.
Older shirts work better, but the difference isn't substantial.
Blink duration also increased, although the difference was not significant.
Again QM QSPR models perform better than EEM QSPR models, but the differences are not substantial.
Nevertheless, these differences are not substantial.
The official said the differences were "not terribly substantial".
The domains supportive care and common drugs in NN showed a decline in the absolute mean difference although this was not substantial.
Although interesting, this difference was not significant.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com