In this study, a novel DEAMOX (DEnitrifying AMmonium OXidation) process coupling anammox with partial-denitrification generated nitrite (NO2−-N) from nitrate (NO3−-N) was developed for simultaneously treating ammonia (NH4+-N) and NO3−-N containing wastewaters. The performance was evaluated in sequencing batch reactors (SBRs) with different carbon sources for partial-denitrification: acetate (R1) and ethanol (R2). Long-term operation (180 days) suggested that desirable nitrogen removal was achieved in both reactors. The performance maintained stably in R1 despite the seasonal decrease of temperature (29.2 °C–12.7 °C), and high nitrogen removal efficiency (NRE) of 93.6% on average was obtained with influent NO3−-N to NH4+-N ratio (NO3−-N/NH4+-N) of 1.0. The anammox process contributed above 95% to total nitrogen (TN) removal in R1 with the nitrate-to-nitrite transformation ratio (NTR) of 95.8% in partial-denitrification. A little lower NRE was observed in R2 with temperature dropped from 90.0% at 22.7 °C to 85.2% at 16.6 °C due to the reduced NTR (87.0%–67.0%). High-throughput sequencing analysis revealed that Thauera genera were dominant in both SBRs (accounted for 61.53% in R1 and 45.17% in R2) and possibly played a key role for partial-denitrification with high NO2−-N accumulation. The Denitratisoma capable of complete denitrification (NO3−-N→N2) was found in R2 that might lead to lower NTR. Furthermore, different anammox species was detected with Candidatus Brocadia and Candidatus Kuenenia in R1, and only Candidatus Kuenenia in R2. Display omitted •Two novel DEAMOX were established for simultaneously treating NH4+-N and NO3−-N.•Stable nitrogen removal efficiency of 93.6% was achieved in acetate-driven DEAMOX.•Nitrogen removal efficiency declined from 90.0% to 85.2% in ethanol-driven DEAMOX.•Genera Thauera (61.53% and 45.17%) would play key role in partial-denitrification.•Brocadia and Kuenenia were identified in acetate-SBR, only Kuenenia in ethanol-SBR.