Little is currently known about preservation of plant DNA in lake sediments. Most prior information originates from laboratory experiments while systematic field-based studies are still lacking. Here, we used the “g” and “h” universal primers for the P6 loop region of the chloroplast trnL (UAA) intron to amplify plant DNA from 219 lake surface sediments from China and Siberia. We introduce (i) the percentage of sequence counts with the best identity ≥95%, (ii) weighted average identity, (iii) weighted average DNA fragment length, and iv) rarefied richness of terrestrial seed plants of plant DNA metabarcoding as proxies for sedimentary DNA preservation and relate them to five environmental variables (lake water conductivity, lake water pH, mean July air temperature, and sampling depth, lake size) using boosted regression tree (BRT) analyses. Our results suggest that lake water chemical characteristics, that is, electrical conductivity and pH, are the most important variables for the preservation of plant DNA in lake sediments. Intermediate water conductivities (100–500 μS cm−1) and neutral to slightly alkaline water pH (7–9) may facilitate plant DNA preservation. Furthermore, deep lakes seem to support plant DNA preservation as indicated by relatively high rarefied richness. We also find high rarefied richness in small lakes compared with large lakes, but this result needs to be assessed by more studies in the future. None of our BRT models shows that mean July air temperature is a key variable to limit plant DNA preservation. To conclude, our results suggest that sedimentary DNA studies can preferentially select deep lakes characterized by intermediate water conductivities and neutral to slightly alkaline pH conditions.