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Customised orthotic insoles play a critical role in addressing foot pathologies and improving comfort and biomechanical alignment for patients with specific needs. The use of 3D printing technology for the manufacturing of orthotic insoles has received considerable attention in recent years due to its potential for customisation, rapid prototyping, and cost-effectiveness. This paper presents the implementation of an algorithm purposely developed to generate an Additive Manufacturing File (AMF) containing the geometry of a patient-specific insole and the stiffness distribution based on pressure analysis from a baropodometric board. The generated file is used to 3D print via Fused Deposition Modelling an insole with a variable infill percentage depending on the pressure distribution on the patient’s foot. Three inputs are used as source data for the AMF file coding: (i) the 3D model that defines the geometry of the insole designed by the orthopaedist; (ii) the pressure map of the patient’s feet obtained with a baropodometric board; and (iii) the stiffness of the material that will be used to fabricate the insole. The proposed approach allows the fabrication of a patient-specific insole, capable of restoring the correct pressure distribution on the foot by varying the infill percentage. Two types of insoles were successfully fabricated using the implemented algorithm: the first was 3D printed, adding a top layer to be ready-to-use; the second was 3D printed without a top surface to be further customised with different coatings. The method described in this paper is robust for the fabrication of customised insoles and aims at overcoming the limitations of the traditional approach based on milling machining (e.g., time, costs, and path planning) since it can be easily integrated into any orthopaedic workshop.