You have to set the harshness of antigen retrieval in relation to the fixation-quality of your tissue. The better the fixation the less sensitive is the tissue.

First of all, what kind of tissue are we talking about? how it is fixed? how many time? wich temperature do you achieve in the microwave?

You can use an histologic bath to control the temperature better...

Is all I can say with no more data.

Preservation of the integrity of morphology in FFPE tissue sections depends on the type of tissue is being used.

May I suggest you to monitor the integrity of tissue morphology in the FFPE tissue sections, prior to conducting IF staining.

Step 1: I suggest that you use a new blade and place the tissue section on pre-coated (++) slides, air dry them preferably overnight, bake the slides at 59 degree Celsius in an air-dry oven for about an hour. Leave the baked slides at ambient temperature for an hour prior to staining them with H & E. This will allow you to monitor the quality of morphology up to this stage. If all is well, then proceed to the IF staining.

Step 2: Allow the slides, after being subjected to AR procedure in a pressure cooker/ microwave oven, to reach the ambient temperature before starting immunostaining. I suppose that pH of the AR solution is no higher than 8.0.

Alternatively, you could use an automatic staining platform (e.g., Leica, Ventana or Dako). They are well designed to perform an AR procedure as well as immunostaining in a mildest possible environment.

You can try doing the antigen retrieval without microwave - put the slides in a coplin jar with citric acid, then put the jar in a 96C bath.

Google it for protocols