Rubuta ci gaba don wannan sakin layi - A ranar 5 ga Disamba, 1990, an yi musayar Alomar da Joe Carter zuwa Toronto Blue Jays a musayar Fred McGriff da Tony Fernández. A Toronto ne ya zama babban dan wasa na biyu, wanda ya hada da.300-plus batting average tare da iko da kuma saurin gudu a kan tushe. A cikin 1991, ya yi amfani da saurin sa tare da sau uku 11 da 53 da aka sace, wanda ya jagoranci tawagar zuwa na farko daga cikin wasanni uku na wasan kwaikwayo. A shekara mai zuwa, ya zira kwallaye 105, ya zana 87 ya yi tafiya, kuma yana da kashi.405 a kan tushe. A cikin 1993, Alomar ya sami mafi kyawun lokacinsa tare da Blue Jays, yana samar da gidaje 17 (HR), 93 ya gudu (RBI), da kuma 55 da aka sace, yayin da yake buga.326, na uku a cikin League na Amurka a bayan abokan wasan John Olerud da Paul Molitor. Ya kasance babban adadi a gasar cin kofin duniya ta Toronto a 1992 da 1993; a wasa na 6 na 1992 World Series, ya zira kwallaye na lashe gasar a kan Dave Winfield na biyu-biyu a karo na 11. Alomar's game-daidaitawa, ninth-inning gida gudu da Oakland taimako ace Dennis Eckersley, a Game 4 na 1992 American League Championship Series
(ALCS), mutane da yawa suna ɗaukarsa a matsayin mafi mahimmancin nasara a tarihin ƙungiyar, kamar yadda tafiye-tafiyen ƙungiyar uku na baya zuwa ALCS suka ƙare cikin takaici; an kira shi Mafi Kyawun Mai Kyau (MVP) na jerin. A cikin 1995, ya buga wasanni 104 a jere ba tare da yin kuskure ba, yana kafa rikodin AL don 'yan wasa na biyu. A cikin kowane yanayi biyar tare da Blue Jays, an kira Alomar zuwa ƙungiyar All-Star kuma ya lashe lambar yabo ta Gold Glove.