Colloids, polymers, gels, and biological materials are widely used for numerous technological applications. The design, fabrication, and understanding of the physico-chemical properties of such (bio)materials, however, represent a challenge for scientists and technologists. This review is a concise update of the latest achievements in surface and bulk analytical techniques applied to biomaterials and soft matter systems. Specific emphasis is devoted to their structural, mechanical, surface, and chemical properties. The review introduces the basics of atomic force microscopy (AFM) and discusses its combination with optical microscopies and spectroscopic techniques. In particular, we report the AFM combination with fluorescence, confocal microscopy, stimulated emission depletion, Raman, and infrared spectroscopy. The review highlights the impact and the potential applications of the combination of such experimental techniques on current problems and questions related to material and polymer science, cell biology, biochemical engineering, and protein chemistry. This review is an accessible introduction to AFM for the newcomer and a source of new experimental information for the experienced researcher.