I am trying to configure a replica set, in Azure Cloud with MongoDB MMS service. I have created a replica set with three nodes, one as primary and two secondaries. How can I make one of those secondary nodes as arbitrary ?
You can't directly "convert" a secondary to an arbiter through replica set reconfiguration. A secondary is a data-bearing node whereas an arbiter is not, so the step of removing a secondary (and dropping data) needs to be explicit.
Via MMS you need to:
The MMS documentation has a tutorial with more detailed steps to Replace a Member with an Arbiter.
It's worth noting the data redundancy impact of having an arbiter in a three node replica set. Technically the fault tolerance of a three node replica set allows any one node to be unavailable and still maintain a primary.
However, if you only have two data-bearing nodes plus an arbiter the impact of a single node being unavailable is different if that node happens to be data-bearing (primary or secondary) versus an arbiter.
If a single unavailable node is data-bearing, then your replica set:
majority
or w:2
write concern)