Context. Protostellar jets are an important agent of star formation feedback, tightly connected with the mass-accretion process. The history of jet formation and mass-ejection provides constraints on the mass accretion history and the nature of the driving source. Aims. We want to characterize the time-variability of the mass-ejection phenomena at work in the Class 0 protostellar phase, in order to better understand the dynamics of the outflowing gas and bring more constraints on the origin of the jet chemical composition and the mass-accretion history. Methods. Using the NOEMA (NOrthern Extended Millimeter Array) interferometer, we have observed the emission of the CO 2-1 and SO N J = 5 4 -4 3 rotational transitions at an angular resolution of 1.0 (820 au) and 0.4 (330 au), respectively, towards the intermediate-mass Class 0 protostellar system Cep E. Results. The CO high-velocity jet emission reveals a central component of ≤ 400 au diameter associated with high-velocity molecular knots, also detected in SO, surrounded by a collimated layer of entrained gas. The gas layer appears to accelerate along the main axis over a length scale δ 0 ≈ 700 au, while its diameter gradually increases up to several 1000 au at 2000 au from the protostar. The jet is fragmented into 18 knots of mass ∼ 10 −3 M , unevenly distributed between the northern and southern lobes, with velocity variations up to 15 km s −1 close to the protostar, well below the jet terminal velocities in the northern (+65 km s −1 ) and southern (−125 km s −1 ) lobes, respectively. The knot interval distribution is approximately bi-modal with a time scale of ∼ 50 − 80 yr close to the jet driving protostar Cep E-A and ∼ 150 − 200 yr at larger distances > 12 . The mass-loss rates derived from knot masses are overall steady, with values of 2.7 × 10 −5 M yr −1 and 8.9 × 10 −6 M yr −1 in the northern and southern lobe, respectively. Conclusions. The interaction of the ambient protostellar material with high-velocity knots drives the formation of a molecular layer around the jet, which accounts for the higher mass-loss rate in the northern lobe. The jet dynamics are well accounted for by a simple precession model with a period of 2000 yr and a mass-ejection period of 55 yr.