Abstract Emissions and efficiency of a pellet boiler (40 kW) at nominal load were compared with emissions and efficiency at reduced load, while fired with six biomass pellets. The pellets include reed canary grass ( Phalaris arundinacea ), pectin waste from citrus shells ( Citrus reticulata ), sunflower husk ( Helianthus annuus ), peat, wheat straw ( Triticum aestivum ) and wood pellets. The measurements of emissions comprised of carbon monoxide (CO), nitrogen oxides (NO x ), sulphur oxides (SO x ) and flue dust mass concentrations (using DIN plus and isokinetic sampling techniques). Emissions varied as a function of operational loads, for each type of pellets. The CO emissions were insignificant with reed canary grass (RCG), citrus pectin waste (CPW) and straw pellets at nominal load, however, at reduced load same pellets emitted 1.9, 4.0 and 7.4 times higher CO than wood pellets, respectively. Peat pellets emitted maximum CO at nominal load (4221.1 mgNm −3 , 12.6 times higher than wood pellets) however; at reduced load CO emission was insignificant. The highest NO x emissions were reported with CPW, which were 3.4 and 4.6 times higher than wood pellets at nominal load and reduced load, respectively. Dust emissions were highest with sunflower husk and lowest with RCG pellets, at both operational modes. The best performance was reported with wood pellets, followed by RCG and pectin pellets, however, wood pellets combustion emitted 1.7 and 2.0 times higher dust DIN plus than RCG at nominal and reduced loads, respectively. Not only fuel specific combustion optimization but also operational load specific optimization is essential for efficient use of agro-pellets in this type of boilers.