Sepsis is a life-threatening condition caused by polymicrobial infections and remains a global health emergency that requires rapid and broad-spectrum diagnostics. Existing CRISPR-based assays face two major limitations that restrict their application for sepsis: narrow protospacer adjacent motif (PAM) site compatibility and poor enzyme stability under clinical and environmental stresses. A modular diagnostic platform is presented, CRISPR-FLEXMO (CRISPR with flexible PAM in metal-organic framework encapsulation, MOF), which integrates a PAM-relaxed Cas12a variant (K607R) with a manganese-coordinated MOF (Mn-MOF) for stable and specific detection of sepsis-causing bacteria. The system targets a conserved region upstream of the Shine-Dalgarno sequence in the 16S rRNA gene containing a universal TTCC PAM, enabling broad-spectrum detection with a single universal primer pair across Gram-negative and Gram-positive pathogens. The K607R variant shows enhanced cis- and trans-cleavage activity, while Mn-MOF encapsulation maintains enzyme functionality under ambient, thermal, and chaotropic stress. The assay detects as low as 10 CFU mL-1 in bacterial lysates following amplification and achieves 100% sensitivity and specificity in serum samples from 15 sepsis patients and 3 healthy individuals, with no cross-reactivity to six respiratory viruses. The platform retains over 78% activity after 12 weeks of room-temperature storage, offering a field-deployable CRISPR diagnostic solution for next-generation infectious disease detection.