Polyester-based scaffolds are of research interest for the regeneration of a wide spectrum of tissues. However, there is a need to improve scaffold wettability and introduce bioactivity. Surface modification is a widely studied approach for improving scaffold performance and maintaining appropriate bulk properties. In this study, three methods to functionalize the surface of the poly(lactide-co-ε-caprolactone) PLCL fibres using gelatin immobilisation were compared. Hydrolysis, oxygen plasma treatment, and aminolysis were chosen as activation methods to introduce carboxyl (-COOH) and amino (-NH2) functional groups on the surface before gelatin immobilisation. To covalently attach the gelatin, carbodiimide coupling was chosen for hydrolysed and plasma-treated materials, and glutaraldehyde crosslinking was used in the case of the aminolysed samples. Materials after physical entrapment of gelatin and immobilisation using carbodiimide coupling without previous activation were prepared as controls. The difference in gelatin amount on the surface, impact on the fibres morphology, molecular weight, and mechanical properties were observed depending on the type of modification and applied parameters of activation. It was shown that hydrolysis influences the surface of the material the most, whereas plasma treatment and aminolysis have an effect on the whole volume of the material. Despite this difference, bulk mechanical properties were affected for all the approaches. All materials were completely hydrophilic after functionalization. Cytotoxicity was not recognized for any of the samples. Gelatin immobilisation resulted in improved L929 cell morphology with the best effect for samples activated with hydrolysis and plasma treatment. Our study indicates that the use of any surface activation method should be limited to the lowest concentration/reaction time that enables subsequent satisfactory functionalization and the decision should be based on a specific function that the final scaffold material has to perform.