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In this paper, a quasi-brittle damage model for micro-architectural materials is presented within the framework of isogeometric analysis to exploit the high-order continuity of the non-uniform B-spline basis functions. The constitutive relation depends not only on the strain field, but also on their first and second strain gradient terms. The simplified second-gradient elasticity formulation from Mindlin’s theory is employed with corresponding micro-architecture-related length scales to capture the material nonlocality and size effects. The strain-based damage is modelled by a nonlocal independent field coupled to the displacement field. Influences of the two types of nonlocalities (manufactured micro-architectures and damage-induced micro-defects) on the response of structures, as well as the damage initiation and propagation, are analysed through numerical experiments. A formula to determine the micro-defect-related length scale from macroscopic measurements is proposed, boosting the accuracy and applicability of the model. In addition, relevant open problems and further developments of this damage model are discussed.