Growing consumer awareness of the importance of food quality on their health is the main driving force for increasing the market for sustainable agricultural products. This makes sustainable, environmentally friendly production methods into non-chemical plant protection products against pathogens, including microbial biopreparations, increasingly important among farmers. Strawberry fruits (Fragaria x ananassa Duch.) are often negatively affected by fungal pathogens. The aim of this study was to evaluate the impact of five combinations of newly developed microbial biopreparations (from K2 to K6) on fungal pathogens and the yield of three strawberry cultivars. The research was conducted on a certified organic strawberry plantation in Poland in 2020–2021. In the first year of the study, no statistically significant positive impact of tested treatments on strawberry yields have been found. At the same time, yields of ‘Honeoye’ treated with K4 combination showed a tendency (with no statistical significance) to have higher yields than the control object by about 33%. In the second year of the study, yields of ‘Honeoye’ and ‘Rumba’ treated with K4 combination (containing Bacillus sp. Sp116AC*, Bacillus sp. Sp115AD, Bacillus sp. AF75BC and Bacillus subtilis AF75AB2, humic acids, yeast culture effluent, micronized dolomite, and mustard and rapeseed oil) significantly increased by 79% and 49%, respectively. Fruit infestation by fungal pathogens was reduced under some microbial treatments; however, the effect varied between years, cultivars, and tested biopreparations. The K2 combination showed a tendency (with no statistical significance) to limit B. cinerea infestation rate by 23% in 2020 and 21% in 2021, C. acutatum by 16% in 2021, and P. cactorum infestation rate by 30% in 2021. Tested microbial biopreparations showed a positive impact on the yield of strawberries and (to some extent) on disease infestation, with an impact on pathogen infestation strongly dependent on the year, variety, and biopreparation tested.