The Ugi four-component condensation in diluted liposomal suspensions was used to prepare pectin-based submicron capsules. A set of isocyanides and aldehydes was used to optimize the synthesis of capsule shells. Modified sugar beet pectin was selected as a natural polymer with pronounced surface activity to create a capsule shell. At first, liposomal composition was optimized in order to select suitable conditions for capsule formation. Then, the wide set of capsules constructed on modified sugar beet pectin scaffold has been synthesized. The choice was determined by level of substitution degree and possible chemical diversity of the modified surface. Detailed characterization of products has been performed for polysaccharide particles with liposomal core prepared with various processing parameters (concentration, cross-linking components, the density of linkage). The chemical structure, average size, polydispersity index, morphology, stability, and cytotoxicity of obtained particles have been investigated in dependence on the shell content. The obtained submicrometer cross-linked capsules (220–240 nm) with controlled colloidal properties showed high stability and low toxicity. Thus, the proposed carriers have a great potential as sustained drug delivery systems for different administration routes. Graphical abstract: [Figure not available: see fulltext.]. © 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.