Aims: We aim to unveil the physical conditions and structure of the intermediate mass (IM) protostar IRAS 21391+5802 (IC 1396 N) on scales of 1000 AU. Methods: We carried out high angular resolution (1farcs4) observations in both the continuum at 3.1 mm and the N2H+ 1 → 0, CH3CN 5k → 4k and 13CS 2 → 1 lines using the Plateau de Bure Interferometer (PdBI). In addition, we merged the PdBI images with previous BIMA (continuum data at 1.2 mm and 3.1 mm) and single-dish (N2H+ 1 → 0) data to obtain a comprehensive description of the region. Results: The combination of our data with BIMA and 30 m data show that the associated bipolar outflow has completely eroded the initial molecular globule. The 1.2 mm and 3.1 mm continuum emissions are extended along the outflow axis tracing the warm walls of the biconical cavity. Most of the molecular gas is, however, located in an elongated feature in the direction perpendicular to the outflow. A strong chemical differentiation is detected across the molecular toroid, the N2H+ 1 → 0 emission being absent in the inner region. Conclusions: Our PdBI data show two different regions in IC 1396 N: (i) the young stellar objects (YSO) BIMA 3 and the protocluster BIMA 2, both were detected in dust continuum emission and one of the individual cores in BIMA 2, IRAM 2A, in the CH3CN 5k → 4k line; and (ii) the clumps and filaments that were only detected in the N2H+ 1 → 0 line. The clumps belonging to this second group are located in the molecular toroid perpendicular to the outflow, and mainly along the walls of the biconical cavity. This chemical differentiation can be understood in terms of the different gas kinetic temperature. The CH3CN abundance towards IRAM 2A is similar to that found in hot corinos and lower than that expected towards IM and high mass hot cores. This indicates that IRAM 2A is a low mass or a Herbig Ae star instead of the precursor of a massive Be star. Alternatively, the low CH3CN abundance could be the consequence of IRAM 2A being a class 0/I transition object that has already formed a small photodissociation region (PDR).