Increasing consumption of processed potatoes and consumer preference for buying potatoes washed and packed in transparent packages are a reason for increasing quality standards for potatoes. Processing and trade require potato tubers with smooth skin and without signs of disease, such as common scab, black scurf, and silver scurf. It is necessary to introduce protective measures to reduce the growth of pathogens causing these diseases and, at the same time, are safe for the environment and the consumer. To meet these requirements, the effects of application to soil and treatment of seed potatoes in the following solutions were examined: biological control agents (BCAs): Pythium oligandrum (BCAPo), Bacillus subtillis str. QST 713 (BCABs); microbial soil additives (MSADs): Efficient microorganisms (EM), UGMax soil conditioner, Biogen Rewital (BR); plant growth promoter (PGP): Ecklonia maxima (PGPEm) for the infection of the tubers by Streptomyces scabies (S.s), Rhizoctonia solani (R.s) Helminthosporium solani (H.s) and potato yield. Average Disease Severity Index (DSI) for common scab (S.s) 62.0%, black scurf (R.s) 57.88%, and silver scurf (H.s) 54.24%, obtained from three growing seasons, indicate their significant economic importance. The bio-preparations used significantly reduced their intensity. The effectiveness of protection for individual pathogens varied and was highly dependent on hydrothermal conditions. The analyzed preparations showed E between 8.0% and 50.8% against S.s. However, a stronger effectiveness was found in relation to H.s (12.9–56.6%) and R.s (19.5–69.2%). In years with water deficit, PGPEm and MSADs are more effective than BCAs in protecting potato tubers from skin diseases and contribute to higher yield increases. There was a significant negative correlation between the total DSI and the potato tuber yield.