Display omitted •A two-stage PN/A system successfully treated undiluted THP/AD dewatering liquor.•Startup by gradually reducing HRT from 20 to 9 h enabled to reach stable PN process.•PN unit operated for 778 days treating high loading rates up to 4.8 g NH4+-N/(L·d).•Inhibitory effects of THP/AD dewatering liquor are removed by the PN reactor itself.•No adverse effect related to the THP/AD process was observed in the anammox reactor. A two-stage system (partial nitritation (PN) and anammox processes) was used to remove nitrogen from the dewatering liquor originating from the thermal hydrolysis/anaerobic digestion (THP/AD) of municipal WWTP sludge. Two strategies were tested to start up the PN reactor: 1) maintaining a fixed hydraulic retention time (HRT) and increasing the ammonium loading rate (ALR) by decreasing the feeding dilution ratio and 2) feeding undiluted dewatering liquor and gradually decreasing the HRT. With diluted feeding, the reactor performance had destabilization episodes that were statistically correlated with the application of high specific ammonium (> 0.6 g NH4+-N/(g TSS·d)) and organic (> 0.7 g COD/(g TSS·d)) loading rates. The second strategy allowed stable PN reactor operation while treating ALR up to 4.8 g NH4+-N/(L·d) and demonstrating that dilution of THP/AD effluents is not required. The operating conditions promoted the presence of free nitrous acid levels (> 0.14 mg HNO2-N/L) inside the PN reactor that inhibited the proliferation of nitrite oxidizing bacteria. Batch activity tests showed that the inhibitory effects of organic compounds present in the THP/AD dewatering liquor on the ammonia oxidizing bacteria activity can be removed in the PN reactor. Thus, aerobic pretreatment would not be necessary when two-stage systems are used. The PN reactor effluent was successfully treated by an anammox reactor. An economic analysis showed that using two-stage systems is advantageous for treating THP/AD dewatering liquor. The implementation of an aerobic pre-treatment unit is recommended for WWTPs capacities higher than 5·105 inhabitants equivalent when one-stage systems are used.