Introduction: Inherited coagulation factor deficiencies (ICFD) result from plasma protein deficiencies, impacting blood coagulation cascade and leading to haemorrhagic diathesis. Advancements in next-generation sequencing (NGS) technology have enabled high-throughput methods for molecular ICFD diagnosis. However, detailed descriptions of clinical applications and routine laboratory experiences in this field remain scarce. Aim: This study presents the results from a real-world experience using an NGS-based gene panel for routine molecular diagnosis, applied to more than 500 ICFD patients in Spain. Methods: A custom NGS gene panel targeting 22 ICFD-related genes was validated using 20 patients with known variants. Subsequently, the panel was applied to 515 ICFD patients from 28 Spanish hospitals. Structural variants were detected by multiplex ligation-dependent probe amplification. Results: Among the 515 patients analysed, 402 had complete phenotypic data specified in the genetic study form, 83 had incomplete data, and 30 were potential haemophilia carriers. Identification disease-causing variant rates were 69%, 58% and 53%, respectively. Candidate variants were identified in 74% of cases. A total of 460 variants across 18 genes were identified, 302 unique variants, with 37% being novel disease-causing variants. Conclusion: This study represents the largest analysis of ICFD patients conducted in Spain, providing significant insights into the molecular epidemiology of these disorders. It underscores the critical role of NGS in routine clinical practice while addressing challenges faced by genetic laboratories. The findings highlight a growing shift among haematologists towards integrating genetic studies early in diagnostic workflows alongside phenotypic assessments to enhance the accuracy and efficiency of ICFD diagnosis.