Tanveer Ahmed, 32, from the Toller district, is accused of killing Asad Shah, 40, outside his convenience store in Glasgow’s Shawlands area on Thursday night.
Ahmed made no plea or declaration at the brief hearing at Glasgow Sheriff Court and was remanded in custody pending a further court appearance.
Police had previously described the incident as a religiously prejudiced attack.
The 40-year-old victim is believed to have been a member of the Ahmadiyya sect of Islam, which preaches peace and tolerance to other religions under the motto Love for All, Hatred for None. He was found seriously injured outside his shop last Thursday night, hours after wishing Christians a happy Easter in a social media post.
Officers confirmed both Mr Shah and the arrested man were Muslims.
Around 150 people gathered on Saturday in the rain to pay their respects to Mr Shah, 40, as floral tributes continued to be laid close to where he was found.
The event, organised by local teenagers on social media, followed a vigil on Friday night attended by a crowd of around 400-500 people, including Scottish First Minister Nicola Sturgeon.
Aleesa Malik, 17, said: “He (Mr Shah) would take the effort to care for every customer.
“He would want to know how are you, what are you doing. He took an interest in everyone’s lives - old, young, anyone.
“You could be any colour, that would not be an issue for him, he just cared too much.”
Nabah Younis, 16, said she had been visiting the shop since she was a young girl.
She described Mr Shah as a “lovely guy”.
Commenting on organising the vigil, she said: “I just felt for the amount of support Mr Shah gave us - us as in Glasgow, Glasgow had to give something in return, and that is exactly what we are doing.”