Herein, we use linker fragmentation approach to introduce boronic acid moieties as functional defects into Zr-based metal organic frameworks (MOFs, UiO-66). Our findings show that the amount of permanently incorporated boronic acid containing ligand is directly dependent on the synthesis method. The accessible boronic acid moieties in the pore surfaces significantly improve the hydrogen uptake values, which are 3.10 and 3.44 wt % at 21 bar, 77 K for dimethylformamide (DMF)/H2O and DMF/HCI synthesis methods, respectively. Also, CO2 selectivity of the resulting MOFs over N-2 and CH4 significantly increases due to the quadrupolar interaction between active surfaces and CO2 molecules. To the best of our knowledge, both hydrogen storage and selectivity of CO2 for UiO-66 are the highest reported values in the literature to date. Furthermore, another striking result that emerged from the high-pressure hydrogen uptake isotherms is the direct correlation between the defects and hysteric adsorption behavior, which may result in the shift from rigidity to flexibility of the framework due to the uncoordinated sites.