To facilitate the ongoing transition towards carbon neutrality, the use of renewable materials for additive manufacturing has become increasingly important. Here, we report for the first time the fabrication of microcapsules from biobased acrylate shells using microfluidics. To select the shell, a wide range of biobased acrylates disclosed in the literature was considered according to their tensile strength, ductile transition temperature and global availability. Once acrylate epoxidised soybean oil (AESO) was selected, its viscosity was adjusted to valuables suitable for the microfluidic device using two different diluting agents. Double emulsions were successfully produced using microfluidics, followed by photopolymerisation of the shell and characterisation of the capsules. Microcapsules containing AESO and isobornyl acrylate (IBOA) were produced with an outer diameter ~490 μm, shell thickness ranging between 36 and 67 μm, and production rates around 2.4 g/h. The mechanical properties of the shell were characterised as tensile strength of 29.2 ± 7.7 MPa, Young’s modulus of 1.7 ± 0.4 GPa and the ductile transition temperature was estimated as 42 °C. To investigate physical triggering, microcapsules produced with a size of 481 ± 4 μm and with a measured shell thickness around 6 μm were embedded in the cementitious matrix. The triggered shells were observed with scanning electron microscopy (SEM) and the uniform distribution of the capsules in cement paste was confirmed using X-ray computed tomography (XCT). These advances can facilitate the wide application of biobased resins for the fabrication of microcapsules for self-healing in cementitious materials.