Camelina sativa (hereafter Camelina) has emerged as a promising platform for metabolic engineering due to its short lifecycle, high seed oil content, and amenability to transformation. Previous work has demonstrated the successful introduction of non‑native pathways for the synthesis of very long chain polyunsaturated fatty acids (VLC‑PUFAs), including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). These achievements required the coordinated expression of up to seven heterologous genes encoding desaturases and elongases from microalgae and other marine organisms. Although the accumulation of EPA and DHA in Camelina seeds has been well characterised, the impact of introducing such a complex pathway on endogenous seed metabolism remains largely unexplored. Here, we apply these two quantitative proteomics strategies to characterise the seed proteomes of elite EPA‑ and DHA‑producing Camelina lines. Our goals were to: 1. assess global proteomic changes associated with multigene engineering. 2. identify proteomic signatures associated with the differing oil‑yield penalties observed in EPA and DHA lines.