If you import col from sqlmodel and wrap the relevant columns with col, the type errors should disappear, at least for the ones in your example:

from sqlmodel import Field, SQLModel, select, col


class TableX(SQLModel, table=True):
    id: int | None = Field(default=None, primary_key=True)
    x: str


class TableY(SQLModel, table=True):
    id: int
    y: str
    z: str


query = (
    select(TableX)
    .join(TableY, col(TableX.id) == col(TableY.id))
    .where(col(TableY.z).in_(["A", "B", "C"]))
)

See:

• Filter Data - WHERE - SQLModel | Type Annotations and Errors¶

• How to use the "IN" clause using the select statement · Issue #353 · fastapi/sqlmodel