This study evaluated the effect of adding Lactiplantibacillus plantarum CNPC003 (LP) and applying milk pasteurization on the microbiological, technological, and physicochemical characteristics and protein profile of artisanal goat coalho cheese during 60 days of ripening. Four types of cheese were produced, including cheeses made with raw and pasteurized goat milk and with and without LP (RC, PC, RCLP, and PCLP). All cheeses were safe for consumption and maintained high lactic acid bacteria counts (above 8 log CFU mL−1) at the end of the ripening period. RC and RCLP showed higher hardness and lower chewiness than cheeses made with pasteurized milk (PC and PCLP) after 60 days of ripening. As expected, there was a reduction in lactose content with a simultaneous increase in acidity and syneresis for all cheeses over the 60 days of ripening, with no significant change in the other evaluated physicochemical parameters. Proteolysis rates increased in all cheeses up to 60 days of ripening, aligning with elevated levels of soluble protein and free amino acids. After 60 days of ripening, PC showed a higher extent of proteolysis index, higher amount of high molecular weight peptides, higher number of identified proteins, and lower content of free amino acids. RCLP showed a higher depth of proteolysis index, higher free amino acids amount (1583 ± 3.95 mg 100 g−1), and fewer identified proteins. Among the peptides identified, it was possible to define 30 potential bioactive peptides according to the bioactivity score (>0.5), where both cheeses added with LP had 18 of these peptides, mostly potentially ACE inhibition sequences. The addition of LP and the pasteurization of milk positively affected the microbiological safety of ripened coalho goat cheeses, primarily contributing to the differentiation of their texture and protein and bioactivity profile.