This paper discusses challenges and obstacles of the Estonian customs authority while implementing the new EU VAT directive aiming to raise efficiency in the VAT declaration life-cycle. The general goal of the directive is to reduce cross-border fraud, gain revenue and modernize the system for governments and businesses. Due to the fact that the impact of the new VAT directive is tremendous, it also changes radically AS-IS work routines of customs authorities. The current paper presents the Estonian experience regarding the implementation of the new work procedures through providing data of the new technology developments and bringing out main concerns in terms of ongoing development activities. Transforming old ICT systems to newer platforms with regards to the new directive also changes current work procedures, which means that adjustments in the organization are also required. The central reason to move towards automatization is the dramatically increasing volumes of shipments requiring customs clearance. However, it is a complex process to achieve this task because of different or non-agreed data sets shared in the existing systems by various stakeholders as well as low quality of data. Consequently, the results of the paper are aimed to aid implementing the changes in various other customs authorities in the EU.