Ah ok now I understand how to do it with

jsonNode.at("/deep/path");

This function returns a JsonNode and you could manipulate it when you cast it to an ObjectNode. If you do that the whole tree get this update.

So my code looks like:

JsonNode jsonNode = new ObjectMapper().valueToTree(myMap);
JsonNode nodeToSetValue = jsonNode.at("/deep/path");
String oldValue = ((ObjectNode) nodeToSetValue).get("finalKey").asText();
String newValue = changeValue(oldValue);
((ObjectNode) nodeToSetValue).put("finalKey", newValue);
myMap = new ObjectMapper().convertValue(jsonNode, new TypeReference<Map<String, Object>>(){}));

The correct json path expression would be "/aaa/0/value1"

Use:

jsonNode.at("/aaa/0/value1")

Yes, the Jackson manual parser design is quite different from other libraries. In particular, you will notice that JsonNode has most of the functions that you would typically associate with array nodes from other APIs. As such, you do not need to cast to an ArrayNode to use. Here's an example:

JSON:

{
    "objects" : ["One", "Two", "Three"]
}

Code:

final String json = "{\"objects\" : [\"One\", \"Two\", \"Three\"]}";

final JsonNode arrNode = new ObjectMapper().readTree(json).get("objects");
if (arrNode.isArray()) {
    for (final JsonNode objNode : arrNode) {
        System.out.println(objNode);
    }
}

Output:

"One"
"Two"
"Three"

Note the use of isArray to verify that the node is actually an array before iterating. The check is not necessary if you are absolutely confident in your data structure, but it's available should you need it (and this is no different from most other JSON libraries).