Baby Daddy follows Ben, a young man in his early 20s living the life of a bachelor in New York City with his buddy, Tucker, and his brother, Danny. Their lives are turned upside down when they come home one day to find a baby girl left on the doorstep by an ex-girlfriend of Ben's. After much deliberation, Ben decides to raise the baby with the help of his friends and his protective and sometimes over-bearing mother, Bonnie, and his close female friend, Riley.
Ben is still enthusiastically searching for the mysterious Elle. Danny and Riley are hunting for a good doctor to help with the pregnancy, and Bonnie desperately wants to be involved. Tucker is back from Los Angeles, but refuses to tell anyone what happened while he was there.
Ben learns some interesting facts about Tucker’s recent date, so he enlists Danny’s help in finding out the truth. As Bonnie and Brad are preparing to set off on their trip around the world, Brad is arrested by the FBI.
When Ben believes he finally has found a no-strings-attached hookup buddy, Riley attempts to prove to him he’s sorely mistaken. Meanwhile, Danny ends up in a professional wrestling match.
Tucker learns that the Mother’s Day special he produced was nominated for a New York Entertainment Award. Tucker’s mom surprises him by showing up to be his plus one to the ceremony, which throws a wrench in Tucker’s plans to have Bonnie pose as his mom. Riley is beginning to show in her pregnancy and worries if this will hold her back from being promoted to junior partner.
Sam comes back into the picture wanting to give her and Ben’s relationship another chance, but Ben hesitates on whether or not that’s a good idea as he’s still searching for the mysterious Elle. Little does he know, Bonnie is hired to be Elle’s new realtor. Danny and Tucker volunteer for a charity ice skating show featuring Emma’s favorite princess, while Riley practices parenting.
Danny is being overprotective of pregnant Riley, so Ben surprises Riley with a day off and a hike in the woods to get some time of freedom. Worried that Ben is too irresponsible, Danny sneaks after them only to learn that Riley is just as scared of becoming a parent as he is. Bonnie learns that her boss may be the reason Brad is in jail, so she schemes with Tucker to gather evidence and set Brad free.
Ben is jealous when he learns Bonnie is sending Danny on a cruise to celebrate becoming a dad, so he and Danny hold a Wheeler War to see who deserves the trip more. Meanwhile, Tucker and Riley run into Tucker’s ex-girlfriend at a Lamaze class. In order to look impressive in front of his ex, Tucker fibs about where he’s at in life which snowballs into a chain of bigger lies and awkward encounters.
Ben meets a runaway bride who is convinced that fate has thrown them together in the same way Ben believes he and Elle are meant to be. Tucker and Ben then figure out how to get out of the situation and back into the good graces of the bridesmaids unscathed. Danny and Riley go on their babymoon cruise, but Bonnie decides to tag along after Danny reveals that he hopes he and Riley will elope.
When Tucker learns that his ex-girlfriend Sondra is newly single, he confides to Ben that she’s the “one that got away.” Ben offers to be Sondra’s rebound to tee Tucker up for success. Bonnie and Riley bond while camping out in a department store to score a sale on a crib. Danny tries to babyproof his and Riley’s apartment do-it-yourself style but seems to break more things than he can fix.
Danny and Ben are eager to find out the sex of Riley and Danny’s baby, even though Riley would prefer it to be a surprise. In their quest to find the truth, the brothers create a chain reaction of mix-ups. Meanwhile, Riley fights for Brad’s innocence in his final trial, and Tucker auditions to be in a new courtroom reality series.
Riley is confined to the couch with the baby due any second while Tucker tries to help Danny decide what to buy her as a “push gift.” Ben begins to feel like an insufficient parent when Emma’s upcoming mother-daughter talent show leads Emma to ask questions about why she doesn’t have a mother.