The current investigation proposes extractive fermentation as a thermodynamically favorable process intensification method for the production and purification of fibrinolytic protease (FLP) from Burkholderia cenocepacia (OK1899609.1) using glycol-based deep eutectic solvents (GDES). Out of the six GDES examined, the recovery rate (97.4%) and the partition coefficient (3.8) were found to be high for GDES 5 (TAC: BC) and sodium sulfate. Brewery liquid waste (BLW) has been utilized as a low-cost carbon source for FLP production yielding 88.5%. Response surface methodology has been performed for optimization of all independent variables such as GDES (20% v/v), salt (15% w/v), BLW (3% v/v), and batch duration of 20 h. The GDES-rich FLP was back extracted and purified by anion exchange chromatography to produce ultrapure fibrinolytic protease (44.6 folds). Thus extractive fermentation of FLP was proved to be thermodynamically favorable and more exergonic results ΔG°E (−8.96 kJ/mol) ΔH°E (6.389 kJ/mol) and ΔS°E (28.70 J/mol). The resultant FLP was also thermostable, as shown by the higher-order activation energy (48.3 kJ/mol), deactivation constant (0.055 min-1), and half-life period (12.6 min). These findings indicate a potential scaling-up of the extractive fermentation from the shaker flask to a large scale with a high recovery of protease and related products.