Companion animals, especially dogs and cats, have increasingly been recognized as moral subjects and valued as family members by European citizens. This new role encourages policy makers to face the many companion animals' welfare issues not yet covered by the EU legislation. The main gaps in the protection of dog and cat welfare during their all lifespan have been identified: unhealthy and unethical breeding practices, irresponsible sale and ownership, transport for commercial and non-commercial purposes, training methods, working dog conditions and rights, regulation of dog and cat shows and competitions, the therapeutic neglect, dog and cat end-of-life care, shelter management legislation and the free-ranging cat and dog population rights. The EU legislation framework is still very weak and far from establishing a harmonized approach, promoting a high standard of care and protection across Member States. We conclude that education and awareness regarding responsible pet ownership and the need for a One Welfare approach have a high value in finding adequate solutions, especially when poor human social welfare affects companion animal welfare. Given the link between human and companion animal welfare, the use of stakeholders' involvement strategies and a transdisciplinary approach appear crucial for the development of an EU legal framework for the well-being of dogs and cats.