Glyphosate and glyphosate-based herbicides are among the most used chemicals in plant pest control. Both glyphosate and its main by-product Aminomethylphosphonic Acid (AMPA) are highly environmentally persistent and, through several processes (including surface runoff and bioaccumulation), affect species beyond their intended targets, especially in aquatic ecosystems. Aedes albopictus is a novel invasive arboviral vector in Colombia and has spread to much of the national territory in recent years. Strains of the bacterium Lysinibacillus sphaericus have shown the ability to degrade glyphosate into environmentally inert compounds, in addition to having great larvicidal efficiency in different mosquito species through the production of several proteins, including the surface layer (S-Layer) protein. The S-Layer is a bacterial structure consisting of glycoprotein monomers, and its functions are thought to include bacterial interactions, protection from the outside medium and biological control. The study assessed the entomopathogenic activity of L. sphaericus S-Layer protein on Ae. albopictus larvae, and the effects that glyphosate and its by-products have in this process. To that end, bioassays were performed to compare the larval mortality between different treatments with and without S-Layer, glyphosate, and glyphosate derivates. Comparisons were made through Analysis of variance (ANOVA) and Tukey’s Honestly Significant Difference (HSD) analyses. Significant differences were found in larval mortality in the treatments, and larval mortality was greater when the S-Layer protein was present, though glyphosate field-doses (1.69 g/L) alone had a notable toxicity as well. An apparent synergic effect on the mortality of larval Ae. albopictus when exposed to mixtures containing 1500 ppm of the S-Layer protein, glyphosate, and/or glyphosate derivates was found. Further studies are needed for the in-depth understanding of this mechanism and its consequences on aquatic ecosystems.