<p>The guinea pig is a key mammal in rural areas of some Andean countries, such as Colombia, where it is an important source of food with high nutritional value that strengthens food security and improves the quality of life of numerous producers, mainly rural women dedicated to guinea pig production. This study investigated Salmonella, Yersinia, and Pasteurella infections in guinea pig production systems at the fattening stage for human consumption in southwestern Colombia, through microbiological, antimicrobial resistance, and histopathological analyses. An observational cross-sectional study was designed in guinea pig farms (<i>n</i> = 100) from the region of Nariño, Cauca, and Putumayo. Samples were collected from smallholder guinea pig farms located in the departments of Nariño, Cauca, and Putumayo, southwestern Colombia. Microbiology samples were taken (sample pool from the three animals on each farm) for culture and identification of Salmonella spp, Yersinia spp, and Pasteurella spp. Antimicrobial susceptibility testing was conducted using the Kirby–Bauer disk diffusion method with isolated bacteria. Additionally, samples were taken for histopathology to validate the presence of histopathological lesions related to the findings of the microbiological examination. In microbiological analysis, the farm distribution for Pasteurella, Yersinia, and Salmonella was 3% (<i>n</i> = 3), 2% (<i>n</i> = 2), and 26% (<i>n</i> = 26), respectively. In the case of Salmonella, this bacterium was identified as Salmonella Typhimurium. Multi-antibiotic resistance was found in these bacteria. In 55% (<i>n</i> = 165) of the animals, histopathological alterations were identified, suggesting local or systemic infections involving other infectious agents different from those evaluated in the present study. Future research should focus on identifying additional pathogens to determine the primary agents associated with infections occurrence in Colombia’s guinea pig meat production systems.</p>