Entity Framework Core 3.1 is throwing a timeout exception for a query that when executed directly is fast

I have a paged query that throws an time-out exception when executed by EF Core 3.1.

Microsoft.Data.SqlClient.SqlException (0x80131904): Execution Timeout Expired. The timeout period elapsed prior to completion of the operation or the server is not responding.

The in-code construction of the query:

Context.Invoices
.Include(i => i.InvoiceLines)
.Include(i => i.InvoiceFiles).ThenInclude(_ => _.File)
.Include(i => i.InvoiceExternalReferences).ThenInclude(_ => _.ReferenceSourceLookup)
.Skip(0).Take(100).AsQueryable()

The query generated by EF Core is:

SELECT
    [t].[Id]
    ,[t].[BookingDateConfirmedUtc]
    ,[t].[BookingDateUtc]
    ,[t].[Checksum]
    ,[t].[Created]
    ,[t].[CreditedInvoiceId]
    ,[t].[CreditingInvoiceId]
    ,[t].[CustomerReference]
    ,[t].[Date]
    ,[t].[ExportDateUtc]
    ,[t].[IsArchived]
    ,[t].[Language]
    ,[t].[LastModified]
    ,[t].[Memo]
    ,[t].[ReceiverId]
    ,[t].[Reference]
    ,[t].[ReferenceFactoryId]
    ,[t].[RelationId]
    ,[t].[SapInvoiceNumber]
    ,[t].[SdBillingDocument]
    ,[t].[SenderId]
    ,[t].[SubType]
    ,[t].[TotalVatAmount]
    ,[t].[Type]
    ,[t].[User]
    ,[t].[UserId]
    ,[t].[VolumeHigh]
    ,[t].[VolumeLow]
    ,[t].[VolumeTotalHours]
    ,[i0].[Id]
    ,[i0].[Amount]
    ,[i0].[AmountRounded]
    ,[i0].[Created]
    ,[i0].[DebugData]
    ,[i0].[Description]
    ,[i0].[FromUtc]
    ,[i0].[InvoiceArticleId]
    ,[i0].[InvoiceId]
    ,[i0].[IsArchived]
    ,[i0].[LastModified]
    ,[i0].[LineNumber]
    ,[i0].[LineType]
    ,[i0].[Price]
    ,[i0].[ProjectConnectionPointId]
    ,[i0].[Quantity]
    ,[i0].[RateCardBillingLineId]
    ,[i0].[ToUtc]
    ,[i0].[Unit]
    ,[i0].[User]
    ,[i0].[UserId]
    ,[i0].[VatPercentage]
    ,[t0].[InvoiceId]
    ,[t0].[FileId]
    ,[t0].[Id]
    ,[t0].[Created]
    ,[t0].[FilePath]
    ,[t0].[FileSize]
    ,[t0].[Filename]
    ,[t0].[IsArchived]
    ,[t0].[LastModified]
    ,[t0].[Remarks]
    ,[t0].[Type]
    ,[t0].[User]
    ,[t0].[UserId]
    ,[t1].[Id]
    ,[t1].[Created]
    ,[t1].[InitialSyncDate]
    ,[t1].[InvoiceId]
    ,[t1].[IsArchived]
    ,[t1].[LastModified]
    ,[t1].[LastSyncDate]
    ,[t1].[Reference]
    ,[t1].[ReferenceSourceLookupId]
    ,[t1].[SyncStatus]
    ,[t1].[User]
    ,[t1].[UserId]
    ,[t1].[Id0]
    ,[t1].[Created0]
    ,[t1].[Dutch]
    ,[t1].[English]
    ,[t1].[French]
    ,[t1].[IsArchived0]
    ,[t1].[IsSystem]
    ,[t1].[LastModified0]
    ,[t1].[Reference0]
    ,[t1].[Type]
    ,[t1].[User0]
    ,[t1].[UserId0]
FROM
(
    SELECT
        [i].[Id]
        ,[i].[BookingDateConfirmedUtc]
        ,[i].[BookingDateUtc]
        ,[i].[Checksum]
        ,[i].[Created]
        ,[i].[CreditedInvoiceId]
        ,[i].[CreditingInvoiceId]
        ,[i].[CustomerReference]
        ,[i].[Date]
        ,[i].[ExportDateUtc]
        ,[i].[IsArchived]
        ,[i].[Language]
        ,[i].[LastModified]
        ,[i].[Memo]
        ,[i].[ReceiverId]
        ,[i].[Reference]
        ,[i].[ReferenceFactoryId]
        ,[i].[RelationId]
        ,[i].[SapInvoiceNumber]
        ,[i].[SdBillingDocument]
        ,[i].[SenderId]
        ,[i].[SubType]
        ,[i].[TotalVatAmount]
        ,[i].[Type]
        ,[i].[User]
        ,[i].[UserId]
        ,[i].[VolumeHigh]
        ,[i].[VolumeLow]
        ,[i].[VolumeTotalHours]
    FROM [Invoices] AS [i]
    WHERE [i].[IsArchived] = CAST(0 AS bit)
    ORDER BY [i].[Reference]
    OFFSET 0 ROWS FETCH NEXT 100 ROWS ONLY
) AS [t]
LEFT JOIN [InvoiceLines] AS [i0] ON [t].[Id] = [i0].[InvoiceId]
LEFT JOIN
(
    SELECT
        [i1].[InvoiceId]
        ,[i1].[FileId]
        ,[f].[Id]
        ,[f].[Created]
        ,[f].[FilePath]
        ,[f].[FileSize]
        ,[f].[Filename]
        ,[f].[IsArchived]
        ,[f].[LastModified]
        ,[f].[Remarks]
        ,[f].[Type]
        ,[f].[User]
        ,[f].[UserId]
    FROM [InvoiceFiles] AS [i1]
    INNER JOIN [Files] AS [f] ON [i1].[FileId] = [f].[Id]
) AS [t0] ON [t].[Id] = [t0].[InvoiceId]
LEFT JOIN
(
    SELECT
        [i2].[Id]
        ,[i2].[Created]
        ,[i2].[InitialSyncDate]
        ,[i2].[InvoiceId]
        ,[i2].[IsArchived]
        ,[i2].[LastModified]
        ,[i2].[LastSyncDate]
        ,[i2].[Reference]
        ,[i2].[ReferenceSourceLookupId]
        ,[i2].[SyncStatus]
        ,[i2].[User]
        ,[i2].[UserId]
        ,[l].[Id] AS [Id0]
        ,[l].[Created] AS [Created0]
        ,[l].[Dutch]
        ,[l].[English]
        ,[l].[French]
        ,[l].[IsArchived] AS [IsArchived0]
        ,[l].[IsSystem]
        ,[l].[LastModified] AS [LastModified0]
        ,[l].[Reference] AS [Reference0]
        ,[l].[Type]
        ,[l].[User] AS [User0]
        ,[l].[UserId] AS [UserId0]
    FROM [InvoiceExternalReferences] AS [i2]
    INNER JOIN [Lookups] AS [l] ON [i2].[ReferenceSourceLookupId] = [l].[Id]
) AS [t1] ON [t].[Id] = [t1].[InvoiceId]
ORDER BY
    [t].[Reference]
    ,[t].[Id]
    ,[i0].[Id]
    ,[t0].[InvoiceId]
    ,[t0].[FileId]
    ,[t0].[Id]
    ,[t1].[Id]
    ,[t1].[Id0]

When I run this query directly to the database, I get an instant result but EF core is throwing a timeout exception.

One potential improvement could be to execute one Load/LoadAsync per each navigation property. Try splitting up the query into multiple Include statements.

var invoices = await context.Invoices
.Include(i => i.InvoiceLines).LoadAsync();

await invoices.Include(i => i.InvoiceFiles).ThenInclude(_ => _.File).LoadAsync();

await invoices.Include(i => i.InvoiceExternalReferences).ThenInclude(_ => _.ReferenceSourceLookup)
.Skip(0).Take(100).ToListAsync();
return invoices.AsQueryable();