The concept of combi-lipases is herein explored in the full hydrolysis of babassu oil. The commercially immobilized lipases from Candida antarctica (form B) (Novozym^® 435), Rhizomucor miehei (Lipozyme^® RM-IM), and Thermomyces lanuginosus (Lipozyme^® TL-IM) were evaluated as single and combined biocatalysts by a mixture design with triangular surface. As a result, after evaluating the response desirability profiling for all biocatalysts, the best biocatalyst in the reaction was the combi-lipases composed of 75% of Lipozyme^® RM-IM, 17% of Novozym^® 435, and 8% of Lipozyme^® TL-IM, reaching full hydrolysis (>99%) after 4 h of reaction. Subsequently, such combi-lipases were employed as biocatalysts in the optimization of the reaction in a shorter reaction time (3 h). After optimization by the Taguchi method, full hydrolysis (>99%) was reached under optimized reaction conditions (9 wt.% of biocatalyst content, 1:2 (oil/water), 40 °C, and 180 rpm). Under such conditions, the combi-lipases maintained 70% of their initial activity after 10 reaction cycles. The antimicrobial activity against some of the most common environmental bacteria of the obtained free fatty acids (FFAs) was also evaluated. The FFAs inhibited more than 90% of the growth of S. aureus, E. coli, and P. aeruginosus when using 10 mg FFAs/mL.