Study objective: We aimed to characterize intra-operative mechanical ventilation with low or high positive end-expiratory pressure (PEEP) and recruitment manoeuvres (RM) regarding intra-tidal recruitment/derecruitment and overdistension using non-linear respiratory mechanics, and mechanical power in obese surgical patients enrolled in the PROBESE trial. Design: Prospective, two-centre substudy of the international, multicentre, two-arm, randomized-controlled PROBESE trial. Setting: Operating rooms of two European University Hospitals. Patients: Forty-eight adult obese patients undergoing abdominal surgery. Interventions: Intra-operative protective ventilation with either PEEP of 12 cmH₂O and repeated RM (HighPEEP+RM) or 4 cmH₂O without RM (LowPEEP). Measurements: The index of intra-tidal recruitment/de-recruitment and overdistension (%E₂) as well as airway pressure, tidal volume (V_T), respiratory rate (RR), resistance, elastance, and mechanical power (MP) were calculated from respiratory signals recorded after anesthesia induction, 1 h thereafter, and end of surgery (EOS). Main results: Twenty-four patients were analyzed in each group. PEEP was higher (mean ± SD, 11.7 ± 0.4 vs. 3.7 ± 0.6 cmH₂O, P < 0.001) and driving pressure lower (12.8 ± 3.5 vs. 21.7 ± 6.8 cmH₂O, P < 0.001) during HighPEEP+RM than LowPEEP, while V_T and RR did not differ significantly (7.3 ± 0.6 vs. 7.4 ± 0.8 ml∙kg⁻¹, P = 0.835; and 14.6 ± 2.5 vs. 15.7 ± 2.0 min⁻¹, P = 0.150, respectively). %E₂ was higher in HighPEEP+RM than in LowPEEP following induction (−3.1 ± 7.2 vs. -12.4 ± 10.2%; P < 0.001) and subsequent timepoints. Total resistance and elastance (13.3 ± 3.8 vs. 17.7 ± 6.8 cmH₂O∙l∙s⁻², P = 0.009; and 15.7 ± 5.5 vs. 28.5 ± 8.4 cmH₂O∙l, P < 0.001, respectively) were lower during HighPEEP+RM than LowPEEP. Additionally, MP was lower in HighPEEP+RM than LowPEEP group (5.0 ± 2.2 vs. 10.4 ± 4.7 J∙min⁻¹, P < 0.001). Conclusions: In this sub-cohort of PROBESE, intra-operative ventilation with high PEEP and RM reduced intra-tidal recruitment/de-recruitment as well as driving pressure, elastance, resistance, and mechanical power, as compared with low PEEP. Trial registration: The PROBESE study was registered at www.clinicaltrials.gov, identifier: NCT02148692 (submission for registration on May 23, 2014).