Climate change is known to disrupt above‐ground food chains when the various trophic layers respond differently to warming. However, little is known about below‐ground food chains involving microbial preys and their predators. Here, we study how climate warming‐induced heat shocks influence resistance (change immediately after a disturbance) and resilience (ability to recover back to pre‐disturbance levels) in rhizosphere microbial communities. We used three species of rhizosphere protists as microbial predators and six different rhizosphere bacterial communities as their prey. Protist species and bacterial communities were extracted from Centaurea stoebe—a range‐expanding plant species in the Northern Europe. We then examined the temporal dynamics of protists and bacterial communities after an extreme heat event for several generations with sufficient recovery periods. We hypothesized that bacterial community resistance and resilience after the extreme heat event would be higher particularly when extreme heat effects would negatively affect their predators. Our results show that prey community biomass was strongly reduced after the extreme heat event and persisted with lower biomass throughout the recovery period. Opposite to what was expected, predators showed negligible changes in their active density after the same heat event. However, abundances of the three predators varied markedly in their temporal dynamics independent of the extreme heat event. Extreme heat event further increased the inactive density of predators, whereas one of the predators showed a decline in its body size owing to extreme heat event. Bacterial community resistance and resilience after the extreme heat event were independent of predator presence, although species‐specific effects of predators on bacterial community resilience were different in the last week of recovery. Predator resilience (based on active predator density) also varied among the three predators but converged over time. Our results highlight that extreme heat events can be more detrimental to microbial prey communities than microbial predators when microbial predators can exhibit thermal acclimation (e.g. change in body size or become inactive) to overcome heat stress. Such thermal acclimation may promote predator resilience after extreme heat events.