Sugar (fatty acid) esters are industrially relevant compounds, with a cumbersome production process due to the solubility issues of the substrates, which forces the use of environmentally unfriendly reaction media. Herein, deep eutectic solvents (DESs) are considered as a promising solution: several literature examples use glucose and different acyl donors to illustrate the efficient synthesis of sugar esters in classic DESs like choline chloride/urea (ChCl/U). However, this paper discloses that when sugars like lactose or other disaccharides are used, enzymes cannot efficiently perform (trans)esterifications in DESs, while the same reaction can proceed in mixtures like pyridine/tetrahydrofuran (Py/THF). This could be explained by computational solubility studies and molecular dynamics simulations of both reaction media, showing two effects: (i) on the one hand, large acyl donors (more than C10) display poor solubility in DESs and (ii) on the other hand, disaccharides interact with DES components. Thus, the DES affects the conformation of lactose (compared to the conformation observed in the Py/THF mixture), in such a way that the enzymatic reaction results impaired. Despite that classic DESs (e.g., ChCl/U) may not be useful for generalizing their use in saccharide ester syntheses, the achieved theoretical understanding of the reaction may enable the design of future DESs that can combine enzyme compatibility with eco-friendliness and efficiency in sugar chemistry.