Decellularized tissues, native or engineered, are receiving increasing interest in the field of regenerative medicine as scaffolds or implants for tissue and organ repair. The approach, which offers the opportunity to deliver off-the-shelf bioactive materials without immuno-matching requirements, is based on the rationale that extracellular matrix (ECM)-presented cues can be potently instructive towards regeneration. However, existing decellularization protocols typically result in damage to the source ECM and do not allow the controlled preservation of its structural, biochemical and/or biomechanical features. Here we propose the deliberate activation of programmed cell death as a method to selectively target the cellular component of a tissue and thereby to preserve the integrity of the decellularized ECM. In the case of engineered tissues, the approach could be complemented by the use of (i) an immortalized cell line, engineered to undergo apoptosis upon exposure to a chemical inducer, and (ii) a perfusion bioreactor system, supporting efficient removal of cellular material. The combination of these tools may lead to the streamlined development of more appropriate materials, based on engineered and decellularized ECM and including a customized set of signals specifically designed to activate endogenous regenerative processes.