ICSI bypasses not only fusion of the gametes but also a series of signalling events that occur in the sperm prior to and during interaction with the oocyte’s vestments. The effect of this altered encounter of the gametes on the fertilization‐associated intracellular calcium ([Ca²⁺]_i) oscillations has not been thoroughly investigated. Here, ICSI and IVF were performed using gametes from two mouse strains, B6D2F1 and CD1, and in‐vitro development, pattern of [Ca²⁺]_i oscillations and down‐regulation of inositol 1,4,5‐trisphosphate receptor‐1 (IP3R‐1) in the produced embryos were compared. ICSI and IVF resulted in comparable rates of activation and pre‐implantation development. However, ICSI‐generated zygotes cleaved at a slower rate, had lower cell numbers and lower hatching rates. The deleterious effects of ICSI could not be exclusively attributed to the injury by the injection since sham‐injected IVF zygotes only exhibited delayed progression to the blastocyst stage. ICSI and IVF induced similar initial [Ca²⁺]_i responses, although ICSI zygotes exhibited shorter durations of [Ca²⁺]_i oscillations and showed diminished degradation of IP3R‐1. Importantly, sperm manipulation affected the pattern of oscillations, which further decreased pre‐implantation developmental rates. Our results demonstrate that ICSI‐induced [Ca²⁺]_i responses are not equivalent to those initiated by IVF and that this may have developmental consequences.