Anthocyanin accumulation in the pericarp and aleuron layers of wheat seed is beneficial for the plant as well as human. Anthocyanin biosynthesis in plants is a complex process, specifically in a polyploid monocot wheat plant and requires the coordinated expression of several regulatory genes. We inspected the transcriptomics comprehensive study of each colored wheat seed (black, blue, and purple) with white wheat in the wheat developmental dough stage. This study's transcriptional signatures and molecular circuitries related to pigmentation patterns revealed different pathways and traits influenced by anthocyanin synthesis in colored wheat seeds. We speculated that at least one isoform of myc and myb transcription factors (TFs) suffices to regulate the anthocyanin synthesis in the pericarp or aleurone of pigmented wheat seeds, while WD 40 showed consecutive expression patterns in all seeds. Through comparative genomics, it was inferred that the advanced black and blue wheat lines used in this study were substitution lines (4E{4D}), with some recombination regions in the distal part, thus performing better than usual complete chromosome substitution lines in terms of agronomic performance. On the other hand, purple wheat performed extremely well agronomically and is equivalent to high-yielding white wheat cultivars as it is only a mutant. Besides that, the transcriptional evidence suggests that pigmented purple pericarp traits are more closely linked with abiotic stress responses. Thus, other environmental stimuli-regulated TFs, linked with various abiotic stress responses, might enhance the pigmentation in the pericarp of wheat seed. Moreover, structural gene expression patterns also change in response to developmental stages, environmental changes, and tissue localization, leading to accumulation of different anthocyanins. Similar observations were also validated through anthocyanin profiling, where different kinds of anthocyanins were observed in black, blue, and purple wheat. Purple wheat showed a higher percentage of acylating genes and acylated anthocyanins.