The first time, Isabelle didn't realize she was pregnant until the day of the abortion. Alec recognized the signs before she did, and brought her to parish vicar and former surgeon - yes, there's a whole story there - Clemency Holt to have the pregnancy terminated. To say Isabelle felt conflicted would be an understatement. She had a breakdown over whether she was supposed to be a good Christian or a good daughter and told Clemency what Alec had been doing to her, but he chose Alec's side, and Isabelle ended up accepting the abortion. I'd give more detail, but I plan on making this a fic, and I don't want to spell out everything. In the end she was left severely traumatized and spiritually damaged, and it's an incredibly painful page of her life she tries to never look back on.

As for the second time, Isabelle was also unaware that she was pregnant until the day of the miscarriage. It was very early in her pregnancy, and while she'd been feeling strange for some time, she didn't put two and two together until she started bleeding. She climbed into the bathtub and waited it out. At first she thought of this as this one a rare act of mercy on God's part, sparing her either having to get an abortion or bringing Alec's child into the world, but soon she was consumed with guilt over that and went once more to Clemency for spiritual guidance over how she should feel after losing her baby. The conversation they then had introduced to Isabelle the idea that the isolation she's locked in with Alec is actually harmful and unnecessary, paving the way for her relationship with Maggie Beth later on.

If Isabelle had stayed, eventually Alec probably would have impregnated her intentionally, but years down the road when she's more physically capable of bearing children. It would be incredibly taxing, especially psychologically. Good thing she got out!