This work applies a multi-scale approach to the microencapsulation by interfacial polymerization. Such microencapsulation is used to produce fertilizers, pesticides and drugs. In this study, variations at three different scales (molecular, microscopic and macroscopic) of product design (i.e., product variables, process variables and properties) are considered simultaneously. We quantify the effect of the formulation, composition and pH change on the microcapsules’ properties. Additionally, the method of measuring the strength of the microcapsules by crushing a sample of microcapsules’ suspension was tested. Results show that the xylene release rate in the microcapsules decreases when the amine functionality is greater due to a stronger crosslinking. Such degree of crosslinking increases the compression force over the microcapsules and improves their appearance. When high levels of amine concentration are used, the initial pH values in the reaction are also high which leads to agglomeration. This study provides a possible explanation to the aggregation based on the kinetic and thermodynamic controls in reactions and shows that the pH measurements account for the polyurea reaction and carbamate formation, which is a reason why this is not a suitable method to study kinetics of polymerization. Finally, the method used to measure the compressive strength of the microcapsules detected differences in formulations and composition with low sensibility.