Intercropping systems combined with the application of organic and biofertilizers can create more sustainable and cleaner plant production systems. This study investigated the effect of organic/biofertilizers and intercropping patterns on the seed yield of ajowan (Carum copticum L.), fenugreek (Trigonella foenum-graecum L.), and pea (Pisum sativum L.) and the essential oil and fatty acid profiles and phenolic compounds of the two medicinal and aromatic plants. The five fertilizer treatments were: no fertilizer (control), 100% chemical fertilizer (NPK), 50% chemical fertilizer+ 100% biofertilizer (CH+B), 50% chemical fertilizer + 100% humic acid (CH+H), and 100% biofertilizer + 100% humic acid (B+H). The six intercropping treatments were ajowan pure stand (Aps), fenugreek pure stand (Fps), pea pure stand (Pps), intercropping one row each of fenugreek + ajowan + pea (1 F:1 A:1 P), intercropping two rows each of fenugreek + ajowan + pea (2 F:2 A:2 P) and intercropping three rows each of fenugreek + ajowan + pea (3 F:3 A:3 P). The results showed that pure stands with CH+H fertilizer produced the highest seed yields for ajowan, fenugreek, and pea, being 29%, 25%, and 30% higher than the unfertilized control. The 2 F:2 A:2 P intercropping ratio fertilized with CH+H had the highest concentrations of ajowan essential oil (3.9%) and main chemical constituents, including thymol (51.3%) and p-cymene (19.6%). The main oil chemical constituents of ajowan included petroselinic acid (69–75.7%) oleic acid (18–23.9%), and palmitic acid (2.1–5.2%). The main chemical constituents of fenugreek oil were linoleic acid (32.4–38.9%), oleic acid (18–24.3%), linolenic acid (16.1–20.9%), and palmitic acid (7.2–14.1%). The 2 F:2 A:2 P intercropping ratio fertilized with CH+H and CH+B had the highest concentrations of coumaric and rosmarinic acids in ajowan and fenugreek, respectively. The results suggest that the 2 F:2 A:2 P intercropping ratio combined with chemical and organic fertilizer application is a more sustainable and cleaner strategy for improving secondary metabolites and fatty acid profiles in ajowan and fenugreek than pure stands.