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Multicellular systems, such as microbial biofilms and cancerous tumors, feature complex biological activities coordinated by cellular interactions mediated via different signaling and regulatory pathways, which are intrinsically heterogeneous, dynamic, and adaptive. However, due to their invasiveness or their inability to interface with native cellular networks, standard bioanalysis methods do not allow in situ spatiotemporal biochemical monitoring of multicellular systems to capture holistic spatiotemporal pictures of systems‐level biology. Here, a high‐throughput reverse nanoimprint lithography approach is reported to create biomimetic transparent nanoplasmonic microporous mesh (BTNMM) devices with ultrathin flexible microporous structures for spatiotemporal multimodal surface‐enhanced Raman spectroscopy (SERS) measurements at the bio‐interface. It is demonstrated that BTNMMs, supporting uniform and ultrasensitive SERS hotspots, can simultaneously enable spatiotemporal multimodal SERS measurements for targeted pH sensing and non‐targeted molecular detection to resolve the diffusion dynamics for pH, adenine, and Rhodamine 6G molecules in agarose gel. Moreover, it is demonstrated that BTNMMs can act as multifunctional bio‐interfaced SERS sensors to conduct in situ spatiotemporal pH mapping and molecular profiling ofEscherichia colibiofilms. It is envisioned that the ultrasensitive multimodal SERS capability, transport permeability, and biomechanical compatibility of the BTNMMs can open exciting avenues for bio‐interfaced multifunctional sensing applications both in vitro and in vivo.