December 5, 1990, Alomar iyo Joe Carter waxaa loo beddelay Toronto Blue Jays si ay ugu beddelaan Fred McGriff iyo Tony Fernández. Waxay aheyd Toronto in uu noqday ciyaaryahanka ugu sareeya ee weerarka labaad, isaga oo isku daraya celcelis ahaan.300 iyo wax ka badan oo leh awood iyo xawaare sare oo ku saabsan saldhigyada. Sanadkii 1991-kii, wuxuu ku guuleystay xawaarihiisii isagoo leh 11 saddex-laable ah iyo 53 saldhig oo la xaday, isagoo kooxda u horseeday kulankiisii ugu horreeyay ee seddex kulan oo isku xigta. Sannadkii xigay, wuxuu dhaliyay 105 runood, wuxuu dhaliyay 87 lug, wuxuuna lahaa boqolkiiba.405 ee salka. Sannadkii 1993, Alomar wuxuu xilli ciyaareedkiisii ugu fiicnaa la qaatay Blue Jays, isagoo soo saaray 17 orod oo gurigiisa ah (HR), 93 orod oo uu ku dhuftay (RBI), iyo 55 saldhigyo la xaday, isagoo garaacaya.326, oo ah kii saddexaad ee Horyaalka Mareykanka oo ka dambeeya asxaabtiisa John Olerud iyo Paul Molitor. Wuxuu ahaa shaqsi muhiim u ah horyaalnimada World Series ee Toronto 1992 iyo 1993; Ciyaarta 6aad ee 1992 World Series, wuxuu dhaliyay orodkii ku guuleystay taxanaha Dave Winfield laba jeer oo laba jeer ah wareega 11aad. Ciyaarta Alomar ee ciyaarta, ciyaarta sagaalaad ee ciyaarta ee Oakland ee Dennis Eckersley, ciyaarta 4aad ee 1992 American League Championship Series
(ALCS), waxaa loo arkaa dad badan inay tahay guushii ugu muhiimsaneyd taariikhda naadiga, maadaama saddexdii safar ee hore ee kooxda ee ALCS ay ku dhammaadeen niyad jab; waxaa loo magacaabay Ciyaaryahanka ugu Qiimaha badan (MVP) ee taxanaha. Sannadkii 1995, wuxuu ciyaaray 104 kulan oo isku xigta isagoon qalad sameyn, isagoo dhigay rikoor AL ah oo loogu talagalay ciyaartoyda lugta labaad. Mid kasta oo ka mid ah shantii xilli ciyaareed ee uu la qaatay Blue Jays, Alomar waxaa loogu magac daray kooxda All-Star wuxuuna ku guuleystay abaalmarinta Golden Glove Award.