Deeply embedded low-mass protostars can be used as testbeds to study the early formation stages of solar-type stars, and the prevailing chemistry before the formation of a planetary system. The present study aims to characterise further the physical and chemical properties of the protostellar core Orion B9-SMM3. The Atacama Pathfinder EXperiment (APEX) telescope was used to perform a follow-up molecular line survey of SMM3. The observations were done using the single pointing (frequency range 218.2-222.2 GHz) and on-the-fly mapping methods (215.1-219.1 GHz). These new data were used in conjunction with our previous data taken by the APEX and Effelsberg 100 m telescopes. The following species were identified from the frequency range 218.2-222.2 GHz:13 CO, C 18 O, SO, para-H 2 CO, and E 1 -type CH 3 OH. The mapping observations revealed that SMM3 is associated with a dense gas core as traced by DCO + and p-H 2 CO. Altogether three different p-H 2 CO transitions were detected with clearly broadened linewidths (∆v ∼ 8.2 − 11 km s −1 in FWHM). The derived p-H 2 CO rotational temperature, 64 ± 15 K, indicates the presence of warm gas. We also detected a narrow p-H 2 CO line (∆v = 0.42 km s −1 ) at the systemic velocity. The p-H 2 CO abundance for the broad component appears to be enhanced by two orders of magnitude with respect to the narrow line value (∼ 3×10 −9 versus ∼ 2×10 −11 ). The detected methanol line shows a linewidth similar to those of the broad p-H 2 CO lines, which indicates their coexistence. The CO isotopologue data suggest that the CO depletion factor decreases from ∼ 27 ± 2 towards the core centre to a value of ∼ 8 ± 1 towards the core edge. In the latter position, the N 2 D + /N 2 H + ratio is revised down to 0.14 ± 0.06. The origin of the subfragments inside the SMM3 core we found previously can be understood in terms of the Jeans instability if non-thermal motions are taken into account. The estimated fragmentation timescale, and the derived chemical abundances suggest that SMM3 is a few times 10 5 yr old, in good agreement with its Class 0 classification inferred from the spectral energy distribution analysis. The broad p-H 2 CO and CH 3 OH lines, and the associated warm gas provide the first clear evidence of a molecular outflow driven by SMM3.