"It feels really bad. It's not just about my personal situation, it's also about the company," he says.
AlNomany, who was brought up in Dubai, received a letter from the agency in October informing him that his work permit would not be extended.
In a repeat of the much debated case of Hussein Ismail, co-founder of Lund's Birka Biostorage, officials at Sweden's Migration Agency judged that there was a discrepancy between the salary AlNomany said he'd receive when he applied for a work permit and the reality.
Linda Krondahl is chief executive of THINGS, the hardware start-up hub at the KTH Royal Institute of Technology, where Inkonova is based. She says almost all company founders at her hub forgo their salaries at some point.
Lisa Bergman, press officer for Sweden's Migration Agency said in a written statement to Radio Sweden that although new case law in Sweden from December now allowed the Migration Agency to make an "overall assessment" in cases where genuine mistakes have been made by employers, "intentional departures from the legal requirements could not be considered to be genuine mistakes."
Alnomy has appealed the decision, but hopes that by publicising his case in the media, politicians will be pushed to again revisit Sweden's regulations around work permits.