•  Malignant Hyperthermia (MH) affects the Ca2+ movements that control muscle contraction. We measured Ca2+ movements in skeletal muscle of “Y522S” mice, with a tyrosine‐to‐serine mutation in the RyR channel that causes MH in mice and humans. •  In YS cells, [Ca2+] inside the Ca2+ store (sarcoplasmic reticulum, SR) was 45% of that in the wild type (WT), but the SR membrane permeability increased 2‐fold, resulting in Ca2+ release of initially normal value. •  During Ca2+release, cytosolic [Ca2+] and SR Ca2+ buffering power evolved differently in YS and WT. These variables became similar in WT exposed to BAPTA, an inhibitor of Ca2+‐dependent inactivation (CDI) of the RyR, suggesting that tyrosine 522 is involved in CDI. •  Similar paradoxical observations in YS and WT cells with reduced content of the SR protein calsequestrin, revealed the importance of balance between SR Ca permeability (increased in YS) and storage capability (decreased when calsequestrin is low). Abstract  Malignant hyperthermia (MH) is linked to mutations in the type 1 ryanodine receptor, RyR1, the Ca2+ channel of the sarcoplasmic reticulum (SR) of skeletal muscle. The Y522S MH mutation was studied for its complex presentation, which includes structurally and functionally altered cell ‘cores’. Imaging cytosolic and intra‐SR [Ca2+] in muscle cells of heterozygous YS mice we determined Ca2+ release flux activated by clamp depolarization, permeability (P) of the SR membrane (ratio of flux and [Ca2+] gradient) and SR Ca2+ buffering power (B). In YS cells resting [Ca2+]SR was 45% of the value in normal littermates (WT). P was more than doubled, so that initial flux was normal. Measuring [Ca2+]SR(t) revealed dynamic changes in B(t). The alterations were similar to those caused by cytosolic BAPTA, which promotes release by hampering Ca2+‐dependent inactivation (CDI). The [Ca2+] transients showed abnormal ‘breaks’, decaying phases after an initial rise, traced to a collapse in flux and P. Similar breaks occurred in WT myofibres with calsequestrin reduced by siRNA; calsequestrin content, however, was normal in YS muscle. Thus, the Y522S mutation causes greater openness of the RyR1, lowers resting [Ca2+]SR and alters SR Ca2+ buffering in a way that copies the functional instability observed upon reduction of calsequestrin content. The similarities with the effects of BAPTA suggest that the mutation, occurring near the cytosolic vestibule of the channel, reduces CDI as one of its primary effects. The unstable SR buffering, mimicked by silencing of calsequestrin, may help precipitate the loss of Ca2+ control that defines a fulminant MH event.