Bryophytes are the second largest taxonomic group in the plant kingdom. They contain a high number of biologically active compounds. Studies of their composition are important for understanding evolutionary processes in the plant kingdom. The aim of this study was to assess bryophyte secondary metabolite extraction options and to increase the yields of polyphenols and substances determining the free radical scavenging activity of bryophyte extracts. Similar studies have been conducted using higher plants as model organisms, but not using bryophytes. Comparison of five extraction methods (conventional, Soxhlet extraction, treatment with microwaves, ultrasound, and supercritical CO2 extraction) and several solvents with differing polarity showed microwave-assisted extraction as the most promising approach to obtain highest yields of extractives. The main factors that contributed to the efficiency of extraction were type of solvent, temperature, and the solvent to bryophyte mass ratio. The extracts obtained from bryophytes had remarkable antioxidant activity, the extent of which depended on the extraction conditions and bryophyte species. The extraction conditions can be optimised, and the total polyphenol content can be increased by up to 50% in comparison with the conventional approach.