We present two comparable diachronic corpora of scientific English and German from the Late Modern Period (17th c.–19th c.) annotated with Universal Dependencies. We describe several steps of data pre-processing and evaluate the resulting parsing accuracy showing how our pre-processing steps significantly improve output quality. As a sanity check for the representativity of our data, we conduct a case study comparing previously gained insights on grammatical change in the scientific genre with our data. Our results reflect the often reported trend of English scientific discourse towards heavy noun phrases and a simplification of the sentence structure (Halliday, 1988; Halliday and Martin, 1993; Biber and Gray, 2011; Biber and Gray, 2016). We also show that this trend applies to German scientific discourse as well. The presented corpora are valuable resources suitable for the contrastive analysis of syntactic diachronic change in the scientific genre between 1650 and 1900. The presented pre-processing procedures and their evaluations are applicable to other languages and can be useful for a variety of Natural Language Processing tasks such as syntactic parsing.