The growth of two pairs of co-cultures (Escherichia coli/Geotrichum candidum and Staphylococcus aureus/Geotrichum candidum) with a starter culture of lactic acid bacteria was studied in milk at temperatures ranging from 15 °C to 21 °C, related to the ripening of artisanal cheese. For an inoculum of approximately 106 CFU/mL, LAB not only induced an early stationary phase of E. coli (two isolates BR and PS2) and S. aureus (isolates 2064 and 14733) but also affected their death phase. In co-cultures with LAB and G. candidum, the numbers of E. coli and S. aureus increased in 2 logs and 1 log, respectively, reaching maximum population densities (MPDs) of less than 5 and 4 logs, respectively. After that, the populations of both bacteria represented with two isolates decreased in more than 2 logs and 3 logs within 2 days compared to their MPDs, respectively. G. candidum was found to be the subject of interactions with LAB within a given temperature range only partially. To develop a tertiary model for the growth curves of the populations, a one-step approach was used, combining the Huang-Gimenez and Dalgaard primary model with secondary square-root models for growth rate and lag time. Furthermore, the reparametrized Gompertz-inspired function with the Bigelow secondary model was used to describe the death phase of the E. coli and S. aureus isolates. The prediction ability of the growth of the H-GD tertiary model for co-cultures was cross-validated within the isolates and datasets in milk and milk medium with 1% NaCl. The study can be used as knowledge support for the hygiene guidelines of short-ripened raw milk cheeses, as was our case in Slovakia.