The statistical experimental design (DoE) and optimization (Response Surface Methodology combined with Box–Behnken design) of sunflower oil transesterification catalyzed by waste chicken eggshell-based catalyst were conducted in a custom-made microreactor at 60 °C. The catalyst was synthesized by the hydration–dehydration method and subsequent calcination at 600 °C. Comprehensive characterization of the obtained catalyst was conducted using: X-ray powder diffractometry (XRD), X-ray fluorescence (XRF), Fourier-transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), N₂ physisorption, and Hg-porosimetry. Structural, morphological, and textural results showed that the obtained catalyst exhibited high porosity and regular dispersity of plate-like CaO as an active species. The obtained optimal residence time, catalyst concentration, and methanol/oil volume ratio for the continuous reaction in microreactor were 10 min, 0.1 g g⁻¹, and 3:1, respectively. The analysis of variance (ANOVA) showed that the obtained reduced quadratic model was adequate for experimental results fitting. The reaction in the microreactor was significantly intensified compared to a conventional batch reactor, as seen through the fatty acid methyl esters (FAMEs) content after 10 min, which was 51.2% and 18.6%, respectively.