Two adults that co-own a residence in Indiana are not married or related in any other way. One needs to apply for Medicaid. Any advice?

Assuming the Deed clearly reads it’s 50/50% ownership, his 50% only will be subject to an after death Recovery action by Medicaid or its outside contractor for MERP.

But imo what will be the more immediate and critical issue will be Medicaids requirement for him to have all his monthly income to be paid to the facility as his copay or SOC (share of cost). If his monthly income is needed to keep all property expenses paid (taxes, insurance, utilities, maintenance etc), then what? 
Can you afford all costs on your own? Due to the SOC it will not be his $. If not married, you can’t get CSRA (Community spouse Resource Allowance... think of this as kinda like alimony for the nonNH spouse). So all property $$$ fall to you.

You need to do whatever to protect your interest & asap. Like some sort of promissory note or Memo of Understanding between you two as to whatever you pay for against his 50% or something else to establish your own claim or lien on the property and as a priority over Medicaid’s. Or you buy out his share based on a valid appraisal. It’s not a DIY, you need an experienced with Medicaid atty., like one that’s NAELA or CELA certified as whatever is done needs to tie into however your states laws read. 

Medicaid will not take the house but it needs to be mentioned in the application. The problem will come when the one owner passes. A lean will be put on the house. If/when the house sells the lean will have to be satisfied. There is more involved but this is basic. This question should be asked when filing.