A 2-year study was carried out in a Croatia to assess the impacts of tillage and fertilisation on soil bulk density (BD), penetration resistance (PR), CO2 emissions and grain yields. The tillage treatments were: conventional tillage (CT), minimum tillage (MT) and reduced tillage (RT). Inside these plots, subplots were fertilised with organic fertiliser, 600 kg ha−1 (CF), 15 t ha−1 (FYM15) and 30 t ha−1 (FYM30) of farmyard manure. In 2017, BD at 10–20 cm was significantly higher in MT than in RT and CT. The same was observed in 2018 at 0–10 cm and 10–20 cm. In 2017, RT had a significantly lower PR than MT and CT. In 2018, PR in RT was significantly lower than MT. In 2017 and 2018 FYM30 and FYM15 application decreased significantly BD in comparison to CF. In 2017, the highest dose of farmyard manure (FYM30 50, 5 kg ha−1 day−1) increased significantly CO2 fluxes comparing to CF (40.7 kg ha−1 day−1). Soil CO2 fluxes under CT (47.9 and 52.3 kg ha−1 day−1 in 2017 and 2018, respectively) were significantly higher than RT (39.1 kg ha−1 day−1) in 2017 and MT (41.7 kg ha−1 day−1) in 2018. Conventional tillage (2.26 t ha−1) had significant lower oat yields than RT (2.72 t ha−1) and MT (2.56 t ha−1). The opposite occurred in barley yields. Farmyard manure significantly increased oat yields in 2017 compared to CF. Overall, reduced tillage with addition of FYM30 can be considered a sustainable management practice, since improved soil physical properties, reduced CO2 fluxes and increased grain yield.