Transduction of many agonists involves mobilization of intracellular Ca2+. The dynamics and shape of intracellular Ca2+ signals are determined by Ca2+ fluxes across the plasma membrane and membranes of intracellular organelles, primarily the endoplasmic reticulum (ER). Although traditionally, intracellular Ca2+ signaling has been studied using chemical fluorescent Ca2+ probes, the advent of genetically encoded Ca2+ sensors with different intracellular localizations has significantly expanded the instrumental capabilities. In the present work, synchronous monitoring of cytosolic Ca2+ in HEK-293 cells using Fluo-8 and of reticular Ca2+ using the genetically encoded ER-localized Ca2+ sensor R-CEPIA1er was performed. Upon stepwise stimulation of cells with acetylcholine (ACh), a coordinated increase in cytosolic Ca2+ and a decrease in ER Ca2+ were observed in the front phase of the Ca2+ response, the relaxation of which was often accompanied by superimposed oscillations. A greater detailing of the correlated behavior of the cytosolic Ca2+ (C) and reticular Ca2+ (Cs) concentrations could be provided by representing cellular responses in the phase plane (Cs, C). Since Cs and C are not measurable directly but evaluated through Ca2+-dependent fluorescence of Ca2+ probes, the experimental data were presented in the (Fs, Fc) plane, where Fs and Fc are ΔF/F0 for R-CEPIA1er and Fluo-8, respectively. Qualitatively, this is equivalent to the presentation of data in the (Cs, C) plane. The phase trajectories indicated that Ca2+ responses to ACh could not be generated solely by Ca2+ exchange between the homogeneous Ca2+ store and the cytosol, since in approximately 30% of cases the phase trajectory contained a loop, wherein a simultaneous increase in Cs and C took place. The loop was observed in a calcium-free medium with negligible Ca2+ influx into the cell, indicating the involvement of an intracellular Ca2+ source that was not accessible to monitoring by R-CEPIA1er or did not significantly contribute to its fluorescence. The inhibitory analysis showed that the suggested source was not acidic endosomes and lysosomes containing two-pore channels, the Golgi apparatus, and vesicles loaded with Ca2+ by SPCA-type ATPase, organelles releasing Ca2+ through ryanodine receptors, and/or mitochondria releasing Ca2+ into the cytosol through the Na+/Ca2+ exchanger. The results obtained pointed out that a system mediating agonist-induced Ca2+ signals is more complex than one in the paradigm with one homogeneous pool of stored Ca2+.