mRNA 5’ caps have many important biological functions, including efficient protein translation and evasion of innate immune response in higher eukaryotes. The primary cap structure, Cap-0, is incorporated by RNA capping enzymes on the 5’ end of mRNA using three distinct enzymatic steps – triphosphatase (TPase), guanylyltransferase (GTase), and N7-methyltransferase (N7MTase). Previous research on RNA capping enzymes focused on characterizing individual enzymes and their activities due to the challenges posed by monitoring multiple substrates and products in the presence of multiple co-substrates in a three-enzyme mechanism. Faustovirus RNA capping enzyme (FCE), like the widely used RNA capping enzyme from Vaccinia virus (VCE), possesses each of the three enzyme activities in separate structural domains. However, FCE is a single chain enzyme and exhibits a higher specific activity and broader temperature range compared to VCE, indicating characteristic differences between their activities. To understand how these multi-functional RNA capping enzymes carry out three sequential enzymatic reactions efficiently, we perform mechanistic research on FCE and VCE using a capillary electrophoresis platform that allows the resolution and quantitation of all three enzyme activities at once. Our studies revealed that while VCE’s TPase activity is over 50-fold faster than FCE’s, its GTase and N7MTase activities are 3- and 8-fold times slower under single turnover conditions, respectively. The GTase single turnover activity is the rate-limiting step of both FCE and VCE, while the N7MTase step is slowest under multiple turnover conditions. Additionally, increasing amounts of Cap-0 slows down the TPase activity, which suggests direct or indirect inhibition between the enzyme’s separate domains. Combined with mutagenesis, protein-ligand binding, and mechanistic modeling, we hope to provide a fuller grasp of these complex multi-functional enzymes and harness their power to advance capped mRNA synthesis technologies.