Any practical realization of entanglement-based quantum communication must be intrinsically secure and able to span long distances avoiding the need of a straight line between the communicating parties. The violation of Bell's inequality offers a method for the certification of quantum links without knowing the inner workings of the devices. Energy-time entanglement quantum communication satisfies all these requirements. However, currently there is a fundamental obstacle with the standard configuration adopted: an intrinsic geometrical loophole that can be exploited to break the security of the communication, in addition to other loopholes. Here we show the first experimental Bell violation with energy-time entanglement distributed over 1 km of optical fibres that is free of this geometrical loophole. This is achieved by adopting a new experimental design, and by using an actively stabilized fibre-based long interferometer. Our results represent an important step towards long-distance secure quantum communication in optical fibres.