This study aimed to reveal the physicochemical and organoleptic effects of three functional LAB isolates in a milk medium: Lacticaseibacillus paracasei subsp. tolerans NOC-122, Levilactobacillus parabrevis NOC-111, and Latilactobacillus curvatus NOC-110. Firstly, a total of 200 indigenous LAB strains isolated from artisanal tulum cheeses were screened for potential proteolytic activity, lipolytic activity, citrate-lyase-synthesizing ability, and EPS-producing ability. Furthermore, a total of six fermentates were produced using these strains as a single culture or as a co-culture with yogurt bacteria. The physicochemical and microbiological properties, the activity of angiotensin-converting enzyme (ACE) inhibitors, and the amino acid and volatile aroma compound profiles of them were determined. In addition, the changes in all these properties during the storage process were determined. According to the results, NOC-110 and NOC-122 were effective in increasing the ACE inhibitory activity. On the other hand, NOC-122 was responsible for a fresh cheesy, slightly oily flavor when used as a single culture. As for the others, NOC-111 gave a fresh, fruity, and slightly herbal flavor; NOC-110 gave a flavor similar to that of NOC-122 when they were used as a single culture. Also, co-cultures of the strains were investigated. The results of the study are a guide for the usability of these isolates as single cultures or co-cultures in the production of dairy-based food. These findings can shed light on many future studies and innovative food products.