Organic farming needs to be promoted as a means of sustaining soil health and reducing the cost of farming, especially for small farmers. The present study deals with the effect of organic compost, prepared using Efficient Microorganism (EM) consortium and applied along with full or half of the recommended dose of chemical fertilizers, on the growth of Calendula and Marigold plants, soil physico-chemical parameters and soil enzyme activities. Soil enzyme activities were improved with the increase in the rate of EM compost application in both Calendula and Marigold. Carotenoid pigment increased by 46.11% and 12.19% with application of EM compost over the control in Calendula and Marigold flowers respectively. Soil humus, available nitrogen and organic carbon content also increased due to the supplementation of EM compost resulting in better soil fertility. For Calendula, treatment T5 (Half dose NPK + EM compost 20 000 kg⋅hm−2) was found to be the most promising in terms of acid phosphatase (82.63 µg p-Nitrophenyl Phosphate⋅g−1⋅h−1), dehydrogenase (10.46 µg Triphenyl Formazan⋅g−1⋅d−1) and β-glucosidase (0.30 IU⋅g−1) activities. In Marigold, treatment C (Half dose NPK + EM compost 5 000 kg⋅hm−2) was the most promising in terms of amendment in soil enzyme activities.