In this work, the effect of the use of two autochthonous starter cultures (Lactobacillus sakei LS131 + Staphylococcus equorum SA25 (EQU), or L. sakei LS131 + Staphylococcus saprophyticus SB12 (SAP)) on the physicochemical, microbiological, proteolytic and lipolytic changes taking place during the manufacture of Galician chorizo, a traditional Spanish sausage, was studied. Three different batches (control (CNT), EQU and SAP) were manufactured in triplicate and analysed during the manufacturing process (samples were taken and analysed at 0, 2, 5, 9, 14, 21 and 30 days of ripening) for proximate composition, pH, aw, colour parameters, nitrogen fractions, free amino acids, biogenic amines, fat parameters and free fatty acids. The use of either of these two starter cultures slightly but significantly reduced the pH values during the fermentation and increased the percentage of transformation to nitrosyl-heme pigments as well as the a* and b* values in the final products. The two starters significantly decreased the Enterobacteriaceae counts in the final product, but without this microbial group completely disappearing. Both starter cultures significantly increased the α-amino acidic nitrogen and the total basic volatile nitrogen fractions during manufacturing, also increasing the free amino acid content and reducing the total biogenic amine content by approximately 20%. The SAP starter enhanced the lipolytic processes, increasing the free fatty acid content. Due to their performances, these two starter cultures seem to be suitable for increasing the quality and safety of the Galician chorizo sausage.