Metaproteomics enables the description of microbial communities (MC). Microbial adaptation to changing environments is conducted by expressing newly synthesized proteins (nP) that can be difficult to distinguish from background proteins. Focusing on nP would add a new dimension to the metaproteomics of MC. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising approach to label nP without significantly influencing the natural behavior of MC. However, direct detection of the BONCAT-labeled nP is limited due to their low abundance compared to total protein. Consequently, enrichment of the BONCAT-labeled nP is essential. We present a workflow using click chemistry (CC) and affinity chromatography to isolate nP from MC. The workflow was developed using a mixture of E. coli (labeled) and yeast (unlabeled control) as a test system. The established workflow was also applied to an MC of a laboratory biogas reactor (LBR).