We examine the main existing challenges that currently arise in the assessment of European Union (EU) funds devoted to three thematic objectives (TOs): Research and Innovation (R&I); Low-carbon economy (LCE); and Information and Communication Technologies (ICT). In this regard, a literature review on the European Regional Development Fund (ERDF) initiatives is performed, with a special focus on the Portuguese (PT) case, also addressing their assessment and reporting practices. Data systematization is coupled with the European Commission (EC)’s main guidelines and with the guidance recommendations brought by Management authorities (MA) for the 2014–2020 period. A bibliometric analysis is conducted to further understand the current research interest in the evaluation of EU funds, and the type of assessment methods and reporting practices employed. Most of the approaches rely on cost–benefit analysis and place less attention on data availability, variable selection, and monitoring/assessment options. The selection and application of the framework indicators, either related to their financial execution or achievement, are assumed as critical factors concerning the monitoring, reporting, and assessment processes. Our findings emphasize the need for harmonization and simplification of the reporting techniques, also highlighting the sparse data availability and some reporting conflicts.