The present research is focused on various pine ecotypes’ seed reproduction in the chalky substrate, challenging environmental conditions on the carbonate soils on chalk outcrops in the south of the Central Russian Upland in relation to pine woods re-afforestation. The winter and spring sowing methods were studied, along with a pre-seeding treatment, by biopreparations based on a consortium of Glomales fungi, bacteria of the genus Bacillus, and bioactive substances. The seeds of two pine ecotypes, Pinus sylvestris L.; Pinus sylvestris var. cretacea Kalenicz exKom, underwent treatment. The study revealed that biopreparations and bioactive substances promote higher pine seed germination rates and ensure the stability and survivability of seedlings in an environment that is unfavorable for plant and tree ontogenesis. Applying biopreparations proved effective during spring sowing, whereas, in the case of winter sowing, their positive impact was not statistically significant. The net effect size of the three organized factors studied in the experiment (pine ecotype, biopreparation, sowing term) (h2x) on the “survivability of P. sylvestris seedlings” effective feature significantly increased from 90.8 to 93.8%. The effect size of the “pine ecotype” factor on seedling survivability in P. sylvestris was at its highest (14.4%) during the seedlings’ first-year growth period. The effect size of the “sowing term” factor was at its highest (79.4%) at the stage of seed germination. The effect size of the “biopreparation” factor was at its highest (44.0%) during the seedlings’ second-year growth stage. Our results indicate that it is preferable to create forest plantations on chalk outcrops using Pinus sylvestris var. cretacea ecotypes and with pre-sowing seed treatment via biopreparations based on a microorganismal consortium and Biogor KM. The Spearman correlation between the nitrification capacity of soil substrate and seedling survivability during the first three growth periods (from planting till the next year’s springtime) was of a moderate size (rs = 0.617–0.673, p < 0.05). To improve the growth and productivity of young and mature Scots pine stands, a Biogeosystem Technique (BGT*) methodology was developed.