In order to highlight the influence of cattle farming systems on dairy products, assessments were carried out on certain varieties of cheese—marked with the “Mountain product” quality label in comparison with those conventionally produced ones not bearing the quality label. The study was carried out using products obtained from raw milk issued from seven farms and transformed into cheese in four small dairy factories from the mountainous area of Dornelor Basin, Suceava County, Northeastern Romania. The analyzed cheese issued from the “mountain” production system were “Călimani” Schweizer, “Călimani” Cașcaval, “Călimani” smoked Cașcaval, and “Călimani” Telemea—salty brined cheese. Both the “Mountain cheese” and conventional cheese samples produced throughout the same shift were collected and kept under refrigeration conditions until laboratory analysis in order to compare the production systems. The physico-chemical analysis revealed higher amounts of minerals (2.8 to 10.7% Ca; 2.8 to 9.5% P; 12.3% to double the amount of Fe, p < 0.001) and polyunsaturated fatty acids (+5.6 to +13.7%), in mountain cheeses versus the conventionally processed ones. Also, the sanogenic indices had higher values in the “Mountain cheese”, such as the polyunsaturation index (+4.3 to 7.8%) and hypocholesterolic/hypercholesterolic fatty acid ratio (+1.8 to 3.7%), while the atherogenic index and the thrombogenic index had lower values (−1.9 to −4.3%) compared to the conventionally produced cheese, thus revealing healthier properties for consumers. The Enterobacteriaceae family species were identified in “Mountain cheese”, while they were absent from conventionally processed cheese, knowing the raw matter milk is thermally treated at ultra-high temperatures in the latter ones. In the “Mountain cheese”, such microorganisms were found within the safety regulation limits and contributed to providing flavor, taste, color, and specific texture, making it superior in terms of sensorial quality compared to the conventionally produced cheese.