Using desi-cow waste products like Jeevamrit under natural farming is widespread among farmers for improving soil biology and productivity. Jeevamrit enhances soil chemical and microbiological properties without needing a large quantity of farmyard manure (FYM) as a sustainable farming practice with a reduced carbon footprint. Despite its traditional use, Jeevamrit faces criticism due to a lack of scientific evidence. This study investigated the comparative effect of Jeevamrit and chemical fertilizers on the growth and yield of marigold cv. Siracole. The experiment employed a randomized block design (RBD) with three replications. The mother block of marigolds was raised for both the summer and winter seasons. From this mother block, three harvesting flushes were taken and propagated from cuttings. The rooted cuttings were planted at monthly intervals and evaluated for flowering parameters and compared to those treated with RDF (30:20:20 N, P, and K g/m2). Soil supplied with Jeevamrit showed enhanced bacteria (26.33%), fungi (18.92%), and actinomycetes (31.21%) populations compared to the recommended dose of fertilizers (RDF) (i.e., N–P–K @ 30:20:20 g m−2). Jeevamrit-treated plants have a more marketable flower yield per square meter (3.98%) and a longer shelf life (9.93%) compared to RDF. The study concludes that Jeevamrit @ 2 liters m−2 is a sustainable and effective alternative to traditional fertilizers for enhancing marigold production in the mid-hills of Himachal Pradesh, where natural farming is already accepted.