Technologies for measuring physiological parameters in vivo offer the possibility of the detection of disease and its progression due to the resulting changes in tissue pH, or temperature, etc.. Here, a compact hydrogel-based optical fibre pH sensor was fabricated, in which polymer microarrays were utilized for the high-throughput discovery of an optimal matrix for pH indicator immobilization. The fabricated hydrogel-based probe responded rapidly to pH changes and demonstrated a good linear correlation within the physiological pH range (from 5.5 to 8.0) with a precision of 0.10 pH units. This miniature probe was validated by measuring pH across a whole ovine lung and allowed discrimination of tumorous and normal tissue, thus offering the potential for the rapid and accurate observation of tissue pH changes.