This study aimed to quantify the carbon footprint (CF) from Fleckvieh cattle production systems in the Amazon region of Peru. Ten farms distributed across four provinces: Chachapoyas (System I; n = 2), Bongara (System II; n = 4), Rodriguez de Mendoza (System III; n = 2), and Utcubamba (System IV; n = 2) were assessed. Parameters such as average live weight, animal units (AU), dry matter intake, fat and protein-corrected milk (FPCM), digestibility, and protein content of consumed forage were analyzed. CF was calculated using the 2019 Refinement to 2006 IPCC guidelines. The database was analyzed using analysis of variance and Duncan’s statistical test (p < 0.05) to compare the systems. A Pearson correlation was carried out to observe the variables association level. Results revealed a CF of 2.50, 2.70 and 2.65 kg CO2eq/kg FPCM by biophysical allocation, according to Global Warming Potential 2007, 2014 and 2021, respectively. Enteric methane (82.6%) and nitrous oxide from manure management (17.2%) were the main contributors to greenhouse gas emissions. Positive correlations were found between methane and nitrous oxide emissions whit total FPCM (r = 0.94), total AU (r = 0.99), and low-producing animals (r = 0.96). System I exhibited the lowest enteric methane emissions, suggesting better livestock and feed management. The study highlights the need to optimize herd composition, increase production levels, and reduce low-producing animals to mitigate CF. Additionally, improving forage quality (increasing the digestibility) enhances milk production, securing the economic well-being of smallholder farmers and agricultural sustainability in the Amazon region.