The effect of fertilization on resistance and resilience of soil microbial activity against heat stress in the tropical soils is largely unknown. We investigated the impact of long‐term (36 years) application of chemical fertilizers and farmyard manure (FYM) on substrate‐induced respiration (SIR) and dehydrogenase activity (DHA) and their resistance and resilience against heat stress in a sandy clay loam soil (Typic Haplustept). Surface soils from five selected treatments (Control, N, NP, NPK, NPK + FYM) under maize (Zea mays) crop were assessed immediately after sampling (0 Day) and at 1, 14, 28 and 56 day(s) after heat stress (48 °C for 24 h). The heat stress significantly decreased soil respiration and dehydrogenase activity by 20–80 %. Recovery after stress was up to 100 % within 56 days. The combined application of NPK (balanced) and FYM was most effective in enhancing resistance and resilience (stability) of soil microbial activity against heat stress. Correlation between resistance of dehydrogenase activity and substrate‐induced respiration revealed a significant relationship (R2 = 0.85). However, after stress, this correlation was initially weak but subsequently improved with time (R2 = 0.38–57), indicating different time lags to restore the normalcy of these parameters.