The aim of this work was to assess whether synthesized random copolyester, poly(butylene terephthalate-r-butylene dilinoleate) (PBT–DLA), containing bio-based components, can effectively compatibilize polypropylene/poly(butylene terephthalate) (PP/PBT) blends. For comparison, a commercial petrochemical triblock copolymer, poly(styrene-b-ethylene/butylene-b-styrene) (SEBS) was used. The chemical structure and block distribution of PBT–DLA was determined using nuclear magnetic resonance spectroscopy and gel permeation chromatography. PP/PBT blends with different mass ratios were prepared via twin-screw extrusion with 5 wt% of each compatibilizer. Thermogravimetric analysis, differential scanning calorimetry, and dynamic mechanical analysis were used to assess changes in phase structure of PP/PBT blends. Static tensile testing demonstrated marked improvement in elongation at break, to ~18% and ~21% for PBT–DLA and SEBS, respectively. Importantly, the morphology of PP/PBT blends compatibilized with PBT–DLA copolymer showed that it is able to act as interphase modifier, being preferentially located at the interface. Therefore, we conclude that by using polycondensation and monomers from renewable resources, it is possible to obtain copolymers that efficiently modify blend miscibility, offering an alternative to widely used, rubber-like petrochemical styrene compatibilizers.