Abstract In the highlands of Madagascar, agricultural expansion gained on grasslands and cropping systems based on direct seeding with permanent vegetation cover are emerging as a means to sustain upland crop production. The objective of this study was to examine how such agricultural practices affect greenhouse‐gas emissions from a loamy Ferralsol previously used as a pasture. We conducted an experiment under controlled laboratory conditions combining cattle manure, crop residues (rice straw), and mineral fertilizers (urea plus NPK or di‐NH 4 ‐phosphate) to mimic on‐field inputs and examined soil CO 2 and N 2 O emissions during a 28‐d incubation at low and high water‐filled pore space (40% and 90% WFPS). Emissions of N 2 O from the control soil , i.e., soil receiving no input, were extremely small (< 5 ng N 2 O‐N (g soil) –1 h –1 ) even under anaerobic conditions. Soil moisture did not affect the order of magnitude of CO 2 emissions while N 2 O fluxes were up to 46 times larger at high soil WFPS, indicating the potential influence of denitrification under these conditions. Both CO 2 and N 2 O emissions were affected by treatments, incubation time, and their interactions. Crop‐residue application resulted in larger fluxes of CO 2 but reduced N 2 O emissions probably due to N immobilization. The use of di‐NH 4 ‐phosphate was a better option than NPK to reduce N 2 O emissions without increasing CO 2 fluxes when soil received mineral fertilizers. Further studies are needed to translate the findings to field conditions and relate greenhouse‐gas budgets to crop production.