Granular organic fertilizers have been increasingly used in agriculture due to the longer delivery of nutrients to plants and the milder impact on the environment. The aim of this study was to determine the energy, environmental and economic efficiency of granular and non-granular organic fertilizers. Four technological scenarios of organic fertilizer use were used for comparative assessment: (1) manure fertilization (16.0 t ha−1), (2) manure fertilization (30.0 t ha−1), (3) manure pellet fertilization (2.0 t ha−1), and (4) fertilization with meat and bone meal pellets (0.7 t ha−1). Experimental studies using the mass flow method of laser spectroscopy were performed to evaluate the comparative environmental impact of granular and non-granular organic fertilizers. Economic assessment was performed for mechanized technological operations of loading, transportation and distribution of organic fertilizers, estimating the price of aggregates used and fuel consumed, the costs of individual technological operations and other indirect costs. The results showed that for mechanized technological operations, when fertilizing with granular organic manure and meat and bone meal fertilizer, energy consumption is 3.2 to 4.0 times lower compared to fertilization with manure. The average ammonia (NH3) emissions from granular organic fertilizers were found to be six times lower than from non-granular organic fertilizers. The lowest costs for mechanized works were incurred when using meat and bone meal pellets, the highest economic benefits of organic fertilizers by elements was when using manure 30 t ha−1, and the highest costs for organic fertilizers were incurred when using manure pellets.