In this paper we present the design and evaluation of a UAV-based system aimed at automating inventory tasks and keeping the traceability of industrial items attached to Radio-Frequency IDentification (RFID) tags. To confront current shortcomings, such a system is developed under a versatile, modular and scalable architecture aimed to reinforce cyber security and decentralization while fostering external audits and big data analytics. Therefore, the system uses a blockchain and a distributed ledger to store certain inventory data collected by UAVs, validate them, ensure their trustworthiness and make them available to the interested parties. In order to show the performance of the proposed system, different tests were performed in a real industrial warehouse, concluding that the system is able to obtain the inventory data really fast in comparison to traditional manual tasks, while being also able to estimate the position of the items when hovering over them thanks to their tag's signal strength. In addition, the performance of the proposed blockchain-based architecture was evaluated in different scenarios.