The existing literature on the Commission has shown that its internal decision-making dynamics vary between legislative proposals. Given the important role of the Commission in the EU legislative process, this variation is likely to have an effect on the subsequent legislative process, as is the case for the internal decision-making of the co-legislators. However, the literature has not yet examined the potential consequences of the Commission intra-institutional process on legislative negotiations. This paper contributes filling this gap by examining the effect of conflicts within the Commission on the extent to which proposals are then amended by legislators. The dependent variable is measured by the extent to which Commission’s proposals are modified by the co-legislators. The comparison of the proposals with the final legislation is done by means of text-mining techniques. More specifically this paper applies the DocuToads algorithm, which has been specifically developed to detect changes between two versions of a legislative text. On this basis, several hypotheses concerning conflicts inside the Commission (e.g. the effect of diverging preferences between DGs) are tested by means of multiple regression techniques. Importantly, the dataset also contains a measure of the difference between the Commission proposal and the positions of the two co-legislators to control for those variables. By assessing whether Commission intra-institutional conflicts are relevant for the final outcomes of the EU legislative process, this paper contributes to a better understanding of both the EU's legislative decision-making process and the Commission's intra-institutional politics. More generally, this paper also contributes empirically to the debate on the Commission's power in EU legislative negotiations.