The zero-range process is a stochastic interacting particle system that is known to exhibit a condensation transition. We present a detailed analysis of this transition in the presence of quenched disorder in the particle interactions. Using rigorous probabilistic arguments we show that disorder changes the critical exponent in the interaction strength below which a condensation transition may occur. The local critical densities may exhibit large fluctuations and their distribution shows an interesting crossover from exponential to algebraic behaviour.