Today’s distributed and pervasive computing addresses large-scale cyber-physical ecosystems, characterised by dense and large networks of devices capable of computation, communication and interaction with the environment and people. While most research focuses on treating these systems as ‘composites’ (i.e., heterogeneous functional complexes), recent developments in fields such as self-organising systems and swarm robotics have opened up a complementary perspective: treating systems as ‘collectives’ (i.e., uniform, collaborative and self-organising groups of entities). This article explores the motivations, state of the art and implications of this ‘collective computing paradigm’ in software engineering. In particular, it discusses its peculiar challenges, implied by characteristics like distribution, situatedness, large scale and cooperative nature. These challenges outline significant directions for future research in software engineering, touching on aspects such as macro-programming, collective intelligence, self-adaptive middleware, learning/synthesis of collective behaviour, human involvement, safety and security in collective cyber-physical ecosystems.