•Stability of lipases in miniemulsions is a key issue to be evaluated.•Secondary structure might be a good parameter to correlate with the drop in activity.•Enzyme unfolding with no secondary structural changes may cause a drop in activity. The exploitation of an efficient enzymatic system to perform biopolymers synthesis, namely polyesters from dicarboxylic acids and dialcohols, requires the evaluation of the enzyme operational stability. This becomes particularly relevant when non-conventional media, such as miniemulsions, are used due to the inhomogeneity of the reaction media and presence of surfactants and high concentrations of organic compounds which might be deleterious to the structure-function of the enzyme. The stability of three lipases, Candida sp., Candida rugosa and Burkholderia cepacia, in miniemulsions during polyester synthesis, was accessed through the secondary structure integrities and activities in order to establish any putative correlations between secondary structure and activity. The effect of the individual components that constitute the emulsion system was also evaluated to identify those which are more disruptive to the secondary structure-function of the enzyme. Depending on the lipase and the presence of different reaction components, three scenarios were observed: a close correlation between secondary structural changes and activity, a drop in activity with no secondary structure alterations but unfolding of tertiary structure and disruption of secondary structure that allows regain of activity in the presence of substrate.