The molecules that make up the bacterial cell wall should be viewed not only as passive structural components of the murein sacculus, which protect and enclose the inner membrane containing the bacterial cytoplasm. They are also bioactive molecules released during bacterial replication, especially after cell lysis, involving the disintegration of the cell wall. These molecules range in structure from simple acetylated monosaccharides or amino acids, such as d-amino acids, to more complex muropeptides and cross-linked peptides. They can be classified as cell wall bioactive molecules (CWBAMs), which have signaling and effector roles that influence bacterial physiology, including biofilm formation, sporulation, and antibiotic resistance. CWBAMs also participate in interactions with other bacteria, the microbiota, and immune cells from human and animal organs, including the central nervous system. The effects of CWBAMs released during cell wall breakdown remain largely unknown, especially since they can translocate from mucosal surfaces colonized by microbiota into the bloodstream. CWBAMs are not necessarily toxins and should be distinguished from endotoxins. Their role in bacterial–host interactions is a promising area for future research.