Aim: To study the carbon fractional status of the growing media and to find out the best organic nitrogen source for fortification of thermochemical organic fertilizer, the manurial constituent of growing media for container cultivation of okra and tomato. Methodology: Container cultivation of okra and tomato were done in completely randomised design. Treatments included fortification with farmyard manure, neem cake, groundnut cake, poultry manure, vermicompost, coir pith compost, hatchery waste organic fertilizer, urea and unfortified thermochemical organic fertilizer. Carbon fractions, viz. total organic carbon, permanganate oxidisable labile carbon, microbial biomass carbon and soil respiration of the growing media were analysed. The yield and yield attributes of the crops were determined. Results: Irrespective of the organic source of nitrogen used, the fortified thermochemical organic fertilizer imparted a high status of total organic carbon to the growing media. Fortification with farmyard manure enhanced labile carbon, soil microbial biomass carbon and soil respiration over those fortified with other organic and inorganic sources. Container grown okra in a growing media with thermochemical organic fertilizer fortified with farmyard manure out yielded urea based fortification by 55.96%. Tomato grown in coir pith compost fortified growing media enhanced yield by 27.37% over the groundnut cake fortified growing media. Linear regression models of labile carbon with microbial biomass carbon (R2 = 0.8946) and with soil respiration (R2 = 0.9053) were significant and with a good fit. Interpretation: Fortification of thermochemical organic fertilizer with various organic sources of nitrogen imparted a high total soil organic carbon status. Synergic effect of the farmyard manure fortification was evident in labile carbon, microbial biomass carbon and soil respiration. Growing media fortified with farmyard manure was ideal for container cultivated okra whereas that with coir pith proved to be ideal for tomato, a solanaceous vegetable crop.